Intelligent Design

We Is Junk

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The quote below is taken from this week’s Nature magazine.

Since joining the blogosphere over two years ago, when challenged, I’ve invoked a scenario pretty much like the one the paper summary is making. I suspect Dave Scot has been making this argument for a longer period than that.

While still preliminary, I have to say that when Nature magazine starts running articles saying that “gene regulation— not the creation of new genes — has moulded the traits that make us unique”, then all that can be said is (a la Allen MacNeil): “Darwinism is dead. Long live evo-devo.” Is the war over?

Anyone who has ever put together self-assembly
furniture knows that having the right parts
is important, but what you do with them can
make or break the project. The same seems
to be true of the vast amounts of DNA in an
organism’s genome that used to be labelled as
junk. Studies now indicate that this DNA may
be responsible for the signals that were crucial
for human evolution, directing the various
components of our genome to work differently
from the way they do in other organisms.

The findings seem to bolster a 30-year-old
hypothesis that gene regulation — not the creation
of new genes — has moulded the traits that
make us unique.

While there’s not many particulars in what I’ve quoted, it strikes me as provocative enough to invite comments. Any takers?

100 Replies to “We Is Junk

  1. 1

    The idea that “Darwinists” are unalterably wedded to the model of “genes” that prevailed in the late 1960s is the strawiest of straw men. Here’s what I recently wrote on this subject in my blog (see: http://evolutionlist.blogspot......-gene.html ):

    For years I have been teaching my students that a gene is a segment of DNA that codes for a single RNA molecule with a complementary sequence, regardless of whether that RNA molecule is translated or not. This definition takes into account the genes for the various rRNAs and tRNAs, which are not translated, and also other forms of non-translated RNA that have recently been discovered. By this definition, genes that code for mRNAs that are actually translated are distinguished as “structural genes,” using terminology that was first developed to describe the Jacob-Monod model of the lactose operon. Using this same terminology, the gene that codes for the lactose repressor protein is a “regulatory gene,” insofar as the repressor does not function in an “extrinsic” biochemical pathway, but rather participates in the regulation of other structural genes.

    However, the distinction between “structural” and “regulatory” genes outlined above is insufficient to describe the various kinds of genetically significant DNA sequences now known. For example, it does not include regions of the DNA to which protein regulators bind, but which are not themselves transcribed. It also does not distinguish between RNAs that are translated into proteins (either enzymes or repressor/regulator proteins) and those that are transcribed into RNA but never translated (such as rRNA, tRNA, and the newer non-translated RNAs).

    Given the foregoing, it appears to me that there are four (possibly five) functionally different kinds of DNA coding sequences:

    (1) translatable sequences: those DNA sequences that are both transcribed into mRNA and later translated into proteins, regardless of function (these can be further subdivided into proteins that participate in non-DNA related biochemical pathways and those that directly regulate DNA, but those seem to me to be classifications of the proteins, not the DNA sequences that code for them);

    (2) transcribable sequences: those DNA sequences that are transcribed into RNA (i.e. rRNA, tRNA, etc.), but are not later translated into proteins/polypeptide chains. Again, what the RNAs do after being transcribed is not a function of the DNA, but rather of the RNAs, and therefore should not really be used to classify DNA coding sequences;

    (3) binding sequences: those DNA sequences that are not transcribed into RNA nor translated into protein, but which function as binding sites for regulatory molecules such as repressor proteins, homeotic gene products, etc. While such sequences do not code for the production of a transcribed or translated gene product, they still participate in the regulation of other genes by serving as regulatory binding sites; and

    (4) non-binding sequences: those DNA sequences that are not transcribed into RNA, not translated into protein, nor function as binding sites for regulatory moelcules. Such sequences would include highly repetitive sequences, tandom repeats, “spacer DNA”, pseudogenes, retroviral and transposon inserts (both “dead” and potentially “alive”), etc. This latter category could be further subdivided into “functional” non-coding/non-binding DNA sequences versus “non-functional/parastitic” non-coding/non-binding DNA sequences, depending on whether they arise as part of the functional architecture of the DNA (primarily of eukaryotes), or whether they arise as side-effects of the action of parasitic genetic elements, such as retroviruses or transposons.

    There may be other categories of DNA sequences that have other functions, but right now I can’t think of any. Therefore, this is how I intend to teach the concept of a “gene” to my students at Cornell from now on.

    So much for the Beadle/Tatum “one gene, one enzyme” model, eh? And the classical Mendelian definition of “one gene, one phenotypic trait” is no longer viable as well…

    And if the Mendelian definition of the gene is now superceded, then the Fisher/Haldane/Wright model of genetic evolution (i.e. the core of the “modern evolutionary synthesis” of the 1930s-50s) has also been superceded.

    But, does this mean that the theory of evolution is dead? Not at all; not any more than relativity theory killed Newtonian mechanics. That’s what happens to scientific theories. Scientists keep discovering new stuff, and the theories change accordingly.

    So, as soon as ID theorists stop spending all their time writing press releases and participating in debates, and start spending time in the field and in the lab doing actual scientific research, there might be a place in science for what they discover. As long as ID theory remains essentially parasitic on biology and the other sciences, it will never be recognized as science. Interpreting other people’s discoveries in the light of different theoretical models doesn’t cut it. That’s why Nobel prizes are awarded to the people making the discoveries, not to the people who figure out what they mean.

    Or, to put it in a way a journalist/literature critic might be able to understand, ID currently stands in relationship to science where literary criticism stands in relationship to literature.

  2. 2
    Jack Golightly says:

    Allen, I can’t help but to appreciate the extensive knowledge and insight you have into this astoundingly complex world of DNA. Thank you for explaining this about the “four (possibly five) functionally different kinds of DNA coding sequences”. Very interesting.
    I have a question though: How does evolutionary theory help you in understanding any of this?

  3. 3
    jpark320 says:

    To be fair only a few supporters of evolution actually know what Dr. MacNeil is talking about… so isn’t it a fair criticism about the supporters of evolution (perhaps not evolution in itself) that tout what Dr. MacNeil describes as a strawman as the truth?

    I think, its harsh to blame IDers for not breaking out much research esp. with the backlash associated with it. We can’t even mention it in fear of alienation and being blacklisted, how are we going to get some lab space to do some research?!?! Mention that you believe in ID in mots labs and you will be frowned upon, let alone given some time to come up with a testable hypothesis.

  4. 4
    jpark320 says:

    To clarify*

    Few supporters = The massive crowd in America that vehemently attack ID, without knowing much evolution themselves.

    Not the upper echelon of biology prof. (though I doubt many of them even know).

  5. 5
    rrf says:

    jpark, if I recall the John Templeton Foundation had made several million dollars available and had solicited proposals for scientific research into ID. Some of that money may still be available.

  6. 6
    Borne says:

    “…ID theorists stop spending all their time writing press … and start spending time in the field and in the lab doing actual scientific research…”

    Here we go again at the very old, useless statement that basically implies that there are no “real” ID scientists in the real, working scientfic community.

    And the Darwimps are constantly doing everythin in their power to keep ANY ID specific realted research from happening. And that by age old terror tactics! It has only gotten worse in the last years.

    The NCSE, Darwin’s “witch-hunters inc.” insure that ID scientists will have hell to pay and blacklisting to suffer for even mentioning or countenancing the idea of proposing real-life ID oriented projects.

    Those who have tried have had evo-priestesses like mme. E. Scott to thank for the evil treatment they’ve received.

    So, what you basically throw out here is worse than a useless challenge. It is also a not so subtle, getting very old and moldly, underlying accusation. The usual one.

    Even more embarassing to you Allen, is this inane statement, “As long as ID theory remains essentially parasitic on biology and the other sciences, it will never be recognized as science.”

    Q: Indeed, and just who do you think is spending millions and working so very hard with such vast and varied low-life tactics at keeping ID out the field?!?
    A: People in the darwinian fundamentalist, “don’t disturb our Lord and Savior, Darwin or be damned”, camp!
    “Darwin loves you”, indeed.

    Your comment is like a tyrant telling his imprisoned victim to show proof of his innocence while still in the dungeon.

    Fortunately the dungeons doors have been shattered & ID is gaining on you Darwinos.

    Much more could be said, considering that most of the great discoveries of science were done by creationists or IDists. Even “natural selection” is an IDists term! The rest I’ll leave to others if they wish to point out the facts to you.

    Pathetic. Shame on you!

  7. 7
    Patrick says:

    So, as soon as ID theorists stop spending all their time writing press releases and participating in debates, and start spending time in the field and in the lab doing actual scientific research, there might be a place in science for what they discover.

    Alan, would you lend your name to support finding funding for additional ID research? I’m sure you believe that line of research will likely turn up fruitless in the end but I think you’d agree it’s at least worth the time to investigate with seriously funded research.

  8. 8
    idnet.com.au says:

    The point of this post seems to be that what ID predicted, that there would be many coded functions contained in the “junk DNA” has proved to be true.

    What random origin theories predict is that there must be a lot of rubbish and junk that is either waiting for some future function or a vestage of some past function.

    We are finding higher and higher level codes in DNA. There is no way that this makes NDE more likely than ID as an explanation.

    The word “evolution” is always inserted somewhere in all these articles otherwise thay would sound like ID papers.

  9. 9
    PaV says:

    Allen MacNeil:

    Interpreting other people’s discoveries in the light of different theoretical models doesn’t cut it. That’s why Nobel prizes are awarded to the people making the discoveries, not to the people who figure out what they mean.

    My sense is that what really happens in labs is that scientists ask themselves this primary and basic question of the life forms they work with: how does it work? They approach and design their work accordingly. Then, once they’ve made some inroad into understanding how something works, they then interpret this in Darwinian terms. IOW, Darwinism is ex post facto. An IDist working in the lab would be asking the same primary and basic question: how does this something work. The difference would be in how the results would be interpreted.

    But, Allen, a question: Were you predicting years ago that they would one day find regulatory elements in so-called “junk DNA”, and did you anticipate that “programming” would be THE major part of determining biological form?

    These are the kinds of things that ID expects. What we read in the scientific literature is one “surprise” after another from Darwinists. I think this is a strong suggestion that conventional evolutionary thinking is off-target, while ID thinking is right on the mark. Why not, as Patrick suggests, work to fund ID research? Or is a hidden materialistic attachment to Darwinism preventing such a thing from happening?

  10. 10
    PaV says:

    One more thing, Allen also wrote:

    Or, to put it in a way a journalist/literature critic might be able to understand, ID currently stands in relationship to science where literary criticism stands in relationship to literature.

    As I’ve noted in the above post, Darwinism is really nothing more than a narrative gloss added to research done in the lab that was motivated by completely non-Darwinian thinking. Hence, IDist are reduced to “critiquing” the gloss. It all fits.

  11. 11
    Michaels7 says:

    Dr. MacNeil,

    A Nobel “Peace” prize was awarded to Yasar Arafat.

    I’m not impressed with their choices as of late.
    You are observing a change in worldviews over time. I’d expect evolutionist to recognize historic reality. We might observe a change of direction back where theist win the bulk of scientific awards as they did so in the past.

    Do you so easily ignore one of the worlds leading genetic scientist, Dr. Sanford? I wonder… is he Nobel worthy? Not that 25 patents in groundbreaking genetic research amount to much. Just surprised you overlook one so near. His work is not considered IDist, but Creationist I guess?

    Has PZ produced any Patents? Dawkins? Dennett? Did a Google search. Four words; “Professor Allen MacNeill patent.” See what the first entry pulls up…
    http://www.google.com/search?q.....S:official
    It was a surprise seeing you listed along with Dr. Sanford.

    Paraphrasing Dr. Sanford, “evolution was a complete waste of his time.”

    MES is superceeded? Old news? I do not remember seeing this announced by evolutionist.

    Lets see, Is MES superceeded?

    October 2005, Abnormal Interest; “Relaxed, clear, informative, straightforward, matter of fact, PZ Myers teaches us about the modern synthesis in biology and debunks Intelligent Designs creationism all in 44 minutes and six
    easy lessons.”

    Is the reviewer totally ignorant of Meyers commentary or is Meyers out of touch with your teachings? I have not listened to the audio, but the review is straight forward.
    Here’s the Link: http://www.telecomtally.com/bl.....n_evo.html

    Or did Modern Synthesis change after October 2005? Maybe its improved…

    From a posting by Esperanza, commenting on the book; Endless Forms Most Beautiful, Chapter 11, by Carroll.

    “Chapter 11 concludes the book with summaries of how Evo devo is so important in biology today. Evo devo is the cornerstone of more modern synthesis. Genes per se were not “drivers” of evolution.””

    So, is Evo Devo the “cornerstone of “more” Modern Synthesis”? Was this predicted by Evolutionist? Or did it take 60 years for it to be recognized? What date did EvoDevo become the “CornerStone” of MES? Or of Evolution for that matter? Certainly that would be in todays high school textbooks, correct? I need to check. Anyone else know?

    As defined, Cornerstone = basis: the fundamental assumptions from which something is begun or developed or calculated or explained; “the whole argument rested on a basis of conjecture”.

    How does a recent discovery become a foundation for “more” of something if the foundation did not exist in the past? Can it be that evolutionist are merely adapting discoveries into their beliefs systems?

    Though I was initially sarcastic in rebuttal to you and for good reason; this is a legitimate question and not offerred as antagonistic.

    Because if the Post at PZ and Carroll are saying EvoDevo is the “Cornerstone” of More Modern Synthesis, but you are saying, MES has been superceeded, then something is not copasetic. We’ve come to a crossroads. And this one’s not in Georgia.

    Which is it? Evo Devo, the Cornerstone of a “More” Modern Syntesis? Or, Superceeded and The Four Gene Types?

    How are IDist, or no, lets stop there and be more direct….

    How am I, supposed to understand Evolutionist when it appears definitions are not formulated clearly within your own scientific community? It certainly is not for a lack of effort in reading the material. I am clearly out of my league with you and others. But pardon me for observing, no wonder there is confusion. If those in the field cannot agree.

    I do not mind being told – We don’t know.

    I realize the general public, myself included can be hard to teach. We do not do this for a living and our knowledge base can be rusty. But I want to make something very clear – that does not translate into – we cannot learn given the same amount of class and lab time. We all take different paths in life.

    And while I do understand how the learned can lose patience with the uninformed. Professors should not lose patience when they themselves cannot present a consistent picture to the students at large.

    Am I wrong in seeing a disconnect within your own community and asking such a straight forward question? It appears to me, monumental changes are taking place.

    Finally Professor MacNeill, you say; “Therefore, this is how I intend to teach the concept of a “gene” to my students at Cornell from now on.”

    You did not teach this concept of genes before now? Do I understood you? I want to know where; “from now on”, enters into your classes as new teaching for genetics material. Did you not teach this in 2005/6 – Fall/Spring/Summer/Fall? And you will be teaching this as “new” material for 2007?

    You have been generous in opening up class time to review of ID.

    For that I am thankful. And I do appreciate your efforts here. But I am curious. Will you teach EvoDevo as the “Cornerstone of More Modern Synthesis” or as Superceeding it?

    Regards…

  12. 12
    Chris Hyland says:

    “We can’t even mention it in fear of alienation and being blacklisted, how are we going to get some lab space to do some research?!?! Mention that you believe in ID in mots labs and you will be frowned upon, let alone given some time to come up with a testable hypothesis.”

    I think the problem with this is that the DI claims it has spent millions on research, and there are supposedly a growing number of scientists who support ID. Johnny B even gave me a list of scientists who are apparently doing ID research so i think it’s unfair to say it’s impossible.

    “Not the upper echelon of biology prof. (though I doubt many of them even know).”

    What Allen said was in one of the first lectures of my degree, and none of the stuff he said or PaV quoted is particularly controversial.

    “Alan, would you lend your name to support finding funding for additional ID research?”

    I think the problem with this is that to my knowledge there are no specific ID research proposals and no indication that anything would come of it. After a decade and supposedly millions spent with next to nothing to show for it people have a right to be sceptical. In any event a lot could be done with a computer and acces to journals so it really isn’t too expensive.

    “The point of this post seems to be that what ID predicted, that there would be many coded functions contained in the “junk DNA” has proved to be true.”

    We’ve known this for decades though. I once worked on investigating functional RNA sequences that came from the ‘junk DNA’ and I had to regularly read papers from th 80s that talked about what Allen is describing. The rate at which we find these things has accelerated exponentially in the last few years though so you hear a lot more about it.

    “We are finding higher and higher level codes in DNA. There is no way that this makes NDE more likely than ID as an explanation.”

    ID will never be seen as an ‘explanation’ until it is fleshed out into a proper theory. Something like the ide of frontloading seems like a small step in the right direction.

    “They approach and design their work accordingly. Then, once they’ve made some inroad into understanding how something works, they then interpret this in Darwinian terms.”

    A lot of them do, a lot of them also use the theory to make predictions about what they will find.

    “Were you predicting years ago that they would one day find regulatory elements in so-called “junk DNA”, and did you anticipate that “programming” would be THE major part of determining biological form?”

    I think people knew about these things before the term ID existed.

    “We might observe a change of direction back where theist win the bulk of scientific awards as they did so in the past.”

    I don’t see how theists winning scientific awards would make a difference. A great number of the people I work with are theists, there are a great number of Evangelicals and other Christians in the royal society in the UK.

    “Has PZ produced any Patents? Dawkins? Dennett?”

    Dont know but I know of a great number of ‘evolutionist scientists’ who have.

    “Which is it? Evo Devo, the Cornerstone of a “More” Modern Synthesis? Or, Superceeded and The Four Gene Types?”

    Both, the modern synthesis has been superseded by a more modern synthesis. The fact that there isnt really standard terminology is annoying but doesn’t change this. Basically evodevo, developmental plasticity, epigenetics and systems biology have expanded the theory. As Allen pointed out this might be analogous to Newtonian gravity being superceeded, but we are still in the transitional phase. I dont expect to see this stuff in highscholl textbooks for at least a few years yet.

  13. 13

    In comment #2, Jack Golightly asked

    “How does evolutionary theory help you in understanding any of this?”

    At its broadest, evolutionary theory encompasses two basic ideas: “descent with modification” (Darwin’s original term for what we now refer to as phylogeny) and “natural selection” (the “mechanism” by which Darwin proposed that descent with modification was caused). Descent with modification is so firmly grounded in empirical observations that even one of the founders of ID (Michael Behe) wholeheartedly supports it. Natural selection, however, is another story.

    According to Darwin, natural selection is the inevitable result of three pre-conditions: variation, inheritance, and fecundity. Given these three pre-conditions, some individuals survive and reproduce more often than others. As a result, their heritable variations become relatively more common over time in the populations of which they are members.

    What many people (including many evolutionary biologists) have often misunderstood is where the real “engine” of evolution is among these preconditions. As John Endler has pointed out, this “engine” isn’t natural selection itself, as it is simply an outcome; a result of the operation of the “engine”. So where is that “engine”, the thing that actually drives the origin and diversification of new phylogenetic lines?

    It is, of course, in the processes that produce new variations. Selection, be it artificial or natural, is limited by whatever variations are present. Furthermore, the effect of selection is to decrease variation, by removing those variations that result in decreased survival and reproduction. So, the “engine” of evolution is really encompassed by those processes that produce variations (i.e. differences) between individuals in populations.

    This is why some astute IDers point to the source of variation as the locus for the operation of the IDesigner. They realize what evolutionary biologists realize: that there is virtually no dispute about the mechanisms of inheritance nor the Malthusian “laws” of fecundity nor the “iron rule” of differential survival and reproduction. The source of all new forms (what Darwin called “endless forms most beautiful”) is the “engines of variation.”

    And so, the reason that evo-devo is sparking a revolution in evolutionary biology is that it provides an empirically testable set of mechanisms for the production of new variation. Notice I said “mechanisms” – i.e. there are many such mechanisms. The ID strawman of “random mutation” hardly encompasses a tiny fraction of what we now recognize as the “engines of variation” the comprise modern genetics and evo-devo.

    Evolutionary biology therefore helps us find these mechanisms by first asserting that they exist. We see overwhelming evidence that descent with modification has occurred, evidence so overwhelming that even the most dedicated IDers agree with it. This requires us to enquire what “mechanisms” must have produced this change. And the answer is, the mechanisms of genetic and developmental variation.

    This summer, our evolution/design seminar spent an evening listing off an briefly describing these mechanisms. We came up with a list of three dozen, everything from single nucleotide point mutations (i.e. substitutions, insertions, and deletions) to whole genome fusion events (such as often happens in hybridization between different species of plants). The list of different ways that variations can be produced is huge and growing, which means that the “engines of variation” are multifarious and extraordinarily effective. And, as far as any current statistical analysis has shown, they are also effectively random. That is, a blizzard of new variations is produced in every generation of every population of organisms. Under natural conditions, selection elminates all but a small fraction of these (under domestication many more survive, as Darwin first proposed).

    So the real question is, are the “engines of variation” sufficient to produce the raw material upon which natural selection operates, producing the adaptations we see in living organisms? So far, based on what we have observed in studying living organisms (and the genetic and developmental mechanisms by which they change over time) the answer is yes.

  14. 14

    As to the question of patents, as I pointed out in my original post, Nobel prizes are awarded for discoveries, not applications (with the exception of the prize for physiology or medicine, which is sometimes awarded to the development of new diagnostic or therapeutic techniques). Therefore, no matter how revolutionary or useful, a new technology such as the one developed by John Sanford will not warrant a Nobel prize. However, a new discovery, such as the 3 degree black body radiation discovered by accident by Penzias and Wilson won them a Nobel prize in physics, even though the full theoretical explanation for the discovery was done by others.

  15. 15
    Joseph says:

    Allen MacNeil:
    Descent with modification is so firmly grounded in empirical observations that even one of the founders of ID (Michael Behe) wholeheartedly supports it.

    It doesn’t matter who supports what. What does matter is what does the data “say”? And guess what? Observational data tells us that wobbling stability is the norm and that only wishful thinking can get around that observation. The bottom-line is sexual reproduction put an end to evolutionism.

    Common descent cannot be objectively tested. It is beyond the realm of modern science to do so for reasons I have provided- the main reason being we do NOT know what makes an organism what it is and we know that although genes may influence every aspect of development they do NOT determine it.

    Allen MacNeil:
    The ID strawman of “random mutation” hardly encompasses a tiny fraction of what we now recognize as the “engines of variation” the comprise modern genetics and evo-devo.

    I would say the “strawman” is all yours- or perhaps you could explain this:

    Mutations are random

    And then we have the following from Dr Spetner discussing transposons:

    The motion of these genetic elements to produce the above mutations has been found to a complex process and we probably haven’t yet discovered all the complexity. But because no one knows why they occur, many geneticists have assumed they occur only by chance. I find it hard to believe that a process as precise and well controlled as the transposition of genetic elements happens only by chance. Some scientists tend to call a mechanism random before we learn what it really does. If the source of the variation for evolution were point mutations, we could say the variation is random. But if the source of the variation is the complex process of transposition, then there is no justification for saying that evolution is based on random events.

  16. 16

    As to the overall question of the value of evolutionary theory to biology, an historical analysis of the development of biology indicates that Darwin’s publication of the Origin of Species in 1859 laid the foundation for the entire science of biology.

    Prior to 1859, there was no “science” of biology in the way that there was a science of physics or chemistry. What Darwin’s predecessors did was called “natural history,” and like history in general, it was virtually entirely descriptive. Science is much more than simple description. It includes an empirical analysis of causes and effects, which are assumed to require only natural causes until the evidence absolutely requires otherwise (which so far hasn’t happened). Darwin’s theory made it possible to investigate the causes of biological diversity, and thereby sparked the formation of the analytical sciences of genetics, developmental biology, comparative anatomy and physiology, paleontology, historical geology, and ecology. By providing an empirically testable hypothesis for the diversity of life, the theory of evolution provided an empirically testable mechanism for biological cause and effect, and initiated the transformation of “natural history” into the modern, evolving science of biology.

  17. 17

    “I find it hard to believe that a process as precise and well controlled as the transposition of genetic elements happens only by chance. ”

    This is what is known as “argument from incredulity” and is no different from Erich von Daniken’s argument that aliens must have built the pyramids and the statues on Easter Island because “it is difficult to believe that such primitive people could have accomplished this.” What a scientist does when confronted with something that she does not understand is to try to figure out a testable natural mechanism (or, preferably several) by which it could have happened, and then perform enough experiments to determine if there is sufficient evidence to eliminate most (or, ideally, all but one) of the possible mechanisms. Only after this has been done is it legitimate to call the explanation that you have proposed a “theory” (i.e. a hypothesis that has been repeatedly teasted, but that has not yet been falsified on the basis of empirical evidence). By this criterion, ID clearly isn’t a theory, it is at best an untested (and perhaps untestable) hypothesis.

  18. 18
    kairos says:

    #15, 19

    So the real question is, are the “engines of variation” sufficient to produce the raw material upon which natural selection operates, producing the adaptations we see in living organisms? So far, based on what we have observed in studying living organisms (and the genetic and developmental mechanisms by which they change over time) the answer is yes.

    Come on Allen; this is pretty wishful thinking. You should know that this confidence on the possibility that “engines of variation” had been able to drive evolution is based on a single observation (the life world such as we can observe it now) and on a classical circular reasoning. The fact that you convince yourself that this could be a real scientific argument does not change the raw fact: apparently no engines of that sort are a plausible explication of life.

    “I find it hard to believe that a process as precise and well controlled as the transposition of genetic elements happens only by chance. ”

    This is what is known as “argument from incredulity” and is no different from Erich von Daniken’s argument that aliens must have built the pyramids and the statues on Easter Island because “it is difficult to believe that such primitive people could have accomplished this.” What a scientist does when confronted with something that she does not understand is to try to figure out a testable natural mechanism (or, preferably several) by which it could have happened, and then perform enough experiments to determine if there is sufficient evidence to eliminate most (or, ideally, all but one) of the possible mechanisms.

    Allen, the argument from incredulity should be supported in a better way (if possible at all). You are missing at least a fundamental point: nobody was so crazy to think that those artifacts could really be the result of natural forces; instead a precise inference of design (bingo!) has always been done and the only problem has been to eventually dispute if this could have been done by past men with their technologies. But this is a quite different point for only few people really think that aliens were the artisans because past men indeedd DID have the capability to design them. Instead the origin of life is “a bit” different if you consider that in this case it is non only a technology problem but, more essentially, a “design of complexity” problem.

    Only after this has been done is it legitimate to call the explanation that you have proposed a “theory” (i.e. a hypothesis that has been repeatedly teasted, but that has not yet been falsified on the basis of empirical evidence). By this criterion, ID clearly isn’t a theory, it is at best an untested (and perhaps untestable) hypothesis.

    It’s strange; if you read NDE for ID, this seems exactly the scientific status of NDE …

  19. 19
    Joseph says:

    “I find it hard to believe that a process as precise and well controlled as the transposition of genetic elements happens only by chance. ”

    Allen MacNeil:
    This is what is known as “argument from incredulity” and is no different from Erich von Daniken’s argument that aliens must have built the pyramids and the statues on Easter Island because “it is difficult to believe that such primitive people could have accomplished this.”

    Alleged “arguments from incredulity” can be refuted by real data. Arguments from ignorance do not count.

    Allen MacNeil:
    What a scientist does when confronted with something that she does not understand is to try to figure out a testable natural mechanism (or, preferably several) by which it could have happened, and then perform enough experiments to determine if there is sufficient evidence to eliminate most (or, ideally, all but one) of the possible mechanisms.

    Dr Spetner has proposed a specific mechansim-> built-in responses to environmental cues, being one. He has also proposed a “non-random evolutionary hypothesis”. So I would suggest getting off of your horse and face reality.

    Allen MacNeil:
    Only after this has been done is it legitimate to call the explanation that you have proposed a “theory” (i.e. a hypothesis that has been repeatedly teasted, but that has not yet been falsified on the basis of empirical evidence). By this criterion, ID clearly isn’t a theory, it is at best an untested (and perhaps untestable) hypothesis.

    But also by that same criterion Common Descent doesn’t qualify and the materialistic alternative to ID, ie sheer-dumb-luck, isn’t even close to qualifying.

    ID can be tested by the concepts of CSI, IC and counterflow.

    Counterflow is how we knew about North Korea’s nuclear blast. And when that is followed back, that is where we find CSI.

    Also “evolution via design” is a mechanism.

    Allen MacNeil:
    Darwin’s theory made it possible to investigate the causes of biological diversity, and thereby sparked the formation of the analytical sciences of genetics, developmental biology, comparative anatomy and physiology, paleontology, historical geology, and ecology.

    IF, Darwin’s theory made it possible to investigate the causes of biological diversity, then why don’t we know what mutations afforded what changes? Why don’t we even know whether or not ANY mutation/ selection process can account for the range of change required for Common Descent to be indicative of reality? And again why is wobbling stability what is actually observed, in nature and in the lab?

  20. 20
    kairos says:

    Sorry, there was an error in quoting a part of Allen’s message. This is the correct text with the answer.:

    ………

    “I find it hard to believe that a process as precise and well controlled as the transposition of genetic elements happens only by chance. ”

    This is what is known as “argument from incredulity” and is no different from Erich von Daniken’s argument that aliens must have built the pyramids and the statues on Easter Island because “it is difficult to believe that such primitive people could have accomplished this.” What a scientist does when confronted with something that she does not understand is to try to figure out a testable natural mechanism (or, preferably several) by which it could have happened, and then perform enough experiments to determine if there is sufficient evidence to eliminate most (or, ideally, all but one) of the possible mechanisms.

    Allen, the argument from incredulity should be supported in a better way (if possible at all). You are missing at least a fundamental point: nobody was so crazy to think that those artifacts could really be the result of natural forces; instead a precise inference of design (bingo!) has always been done and the only problem has been to eventually dispute if this could have been done by past men with their technologies. But this is a quite different point for only few people really think that aliens were the artisans because past men indeedd DID have the capability to design them. Instead the origin of life is “a bit” different if you consider that in this case it is non only a technology problem but, more essentially, a “design of complexity” problem.
    ……..

  21. 21

    Joseph asked:

    “…why don’t we know what mutations afforded what changes? ”

    Actually, we do. As just one example, we know that a fusion of two chromosomes in a primate ancestor in the hominid line is correlated with the divergence between the line that led to humans and the line that led to chimps and other great apes. We know this because human chromosome #2 is the product of this fusion, a conclusion that is based on pure empirical genetic testing.

    Joseph also asked:

    “Why don’t we even know whether or not ANY mutation/ selection process can account for the range of change required for Common Descent to be indicative of reality?”

    We don’t yet know whether or not variation coupled with inheritance, fecundity, and resulting in differential survival and reproduction has done this because we are still investigating such possibilities. That’s what science is all about: doing the hard work in the field and in the lab that either falsifies one’s hypotheses or not.

    Referring to CSI, IC, and other ID ideas isn’t doing science at all. It does not involve doing actual experiments or field observations, it simply relies upon conceptual arguements, arguments that so far have no empirical support. Until IDers start performing actual experiments or gathering field data that clearly and unambiguously distinguish between EB and ID hypotheses, evolutionary biologists will continue to assert (with a century and a half of empirical evidence to back them up) that ID “theories” (which to date are no more than hypotheses) have no empirical support, and are therefore not science.

  22. 22
    kairos says:

    #23

    Referring to CSI, IC, and other ID ideas isn’t doing science at all. It does not involve doing actual experiments or field observations, it simply relies upon conceptual arguements, arguments that so far have no empirical support.

    The “conceptual arguments” you are referring are just based on the strongest and clearest empirical support: evidence of complexity and specificity (as far as known only realized by intelligent agencies) and huge experimental inability of the proposed undriven mechanisms to decently account for them. BTW, all science you are speaking about does really describe thinks that suggest evolution did occur but NOT how evolution did occur. Moreover,
    surely you know that since tens of years mathematicians have strongly criticized the optimistical and wishful claims coming from biologists used to sell NDE without an even small probabilistic proof. Apparently you are simply going on the same way.

    Until IDers start performing actual experiments or gathering field data that clearly and unambiguously distinguish between EB and ID hypotheses, evolutionary biologists will continue to assert (with a century and a half of empirical evidence to back them up) that ID “theories” (which to date are no more than hypotheses) have no empirical support, and are therefore not science.

    But 150 years ago they thought cells were a mere biological jello; as you know things are now MORE AND MORE worse for susch a sort of speculations.

  23. 23
    JasonTheGreek says:

    More bunk from Al here.

    First notice the extreme arrogance. I wonder what his students feel like- knowing they’re all so far below him…?

    Al wrote:
    “Actually, we do. As just one example, we know that a fusion of two chromosomes in a primate ancestor in the hominid line is correlated with the divergence between the line that led to humans and the line that led to chimps and other great apes. We know this because human chromosome #2 is the product of this fusion, a conclusion that is based on pure empirical genetic testing.”

    This doesn’t make any sense. We cannot genetically test the supposed last common ancestor, because we have no idea what it might have been. Chromosome #2 APPEARS to be a product of fusion, but this cannot, in ANY manner, be tested in any empirical manner. You can PROPOSE a fusion event, but you can’t test it out. Mapping the chimp and human genomes won’t help you out here either.

    Furthermore, there’s NO way to test WHEN this supposed event took place. Let’s say, for argument’s sake, it IS a fusion event. We have no idea when it took place in time, where at in the ‘line’ from hominid to chimp to human, etc.

    He ends his comment with the usual fluff- ID isn’t science, IDers aren’t true scientists, they refuse to do lab work, they refuse to practice TRUE science, etc.

    If experimentation is what makes an idea science- I guess that means the idea of black holes aren’t considered science. There are MANY things in science which cannot be tested empircally. A transition from one species to another is a prime example of what cannot be tested (Darwinists: “it would take far longer to show this than any human can live!”) Don’t buy the nonsense- experimentation doesn’t equal science in the manner Al claims. No one has done an experiment to show common descent, so this very idea would be thrown our with Allen’s double standards.

  24. 24
    JasonTheGreek says:

    Look on the bright side th0- at least ol’ white brows hasn’t called us all anti-science fools as he did in a previous comment!

  25. 25
    PaV says:

    Allen MacNeil:

    So the real question is, are the “engines of variation” sufficient to produce the raw material upon which natural selection operates, producing the adaptations we see in living organisms? So far, based on what we have observed in studying living organisms (and the genetic and developmental mechanisms by which they change over time) the answer is yes.

    Allen, it’s always nice to have you here posting. You fight fair; i.e., you punch us in the nose, but you don’t kick us in the ribs.

    I’d like to take a “jab” at you right now if I can.

    Specifically, I disagree 1000% with what you identify as the “real question”. The “real question” is not if the “engines of variation” are sufficient to produce the raw material upon which NS operates. The answer to that question is obviously “yes”, since the world is full of variable species. The “real question” is this : Do the “engines of variation” provide sufficient variation to move beyond microevolution to macroevolution.

    That still is the debate here. I can’t tell you how happy I am not to have people forcing RM+NS down my throat as THE answer to evolutionary diversity. Nonetheless, conceding the three dozen mechanisms of variation, there still remains the question of whether these “dozens” of mechanism can be “orchestrated” in such a way as to bring about large-scale changes in organisms. It would seem that Goldschmidt’s “hopeful monster” would be just the kind of thing you’d be latching onto right now. Yet, even that doesn’t get you out of the woods, since there now is this problem of “information systems”. More and more, what we see coming out of labs these days is affirmation of DNA/RNA as a developmental program much like that of a computer program—only vastly more complex. The problem to be solved, and the question to be answered, is: can NS, acting alone, bring about a “rearrangement” of the “genetic program” of a particular organism. I, for one, accept the “fact” of evolution (i.e., the fossil record), and I conditionally accept “common descent” (stochastic, versus continuous, descent has not been ruled out; but this is but a fine point), and I accept that there are many “mechanisms of variability”, but logically Darwinian evolution (i.e., variability, inheritance, fecundity) seems completely impotent in “stochastically” arriving at a new “program mode” for DNA/RNA information systems.

  26. 26
    JasonTheGreek says:

    By the way- if you go to dr. al’s blog- his top post is about atheism. Wait- I thought Darwinism didn’t equal atheism? (gasp!) He shows his true colors when he says this of religion and science:

    “Don’t get me wrong: I don’t begrudge religious believers their beliefs. But, if I had to make a choice and my life (or the life of someone I loved) were on the line, I would choose science every time. In other words, if it were a choice between a deeply religious but poorly trained doctor without much “bedside manner” and an atheist but highly trained doctor with the bedside manner of a Marine drill sargeant, I would choose the latter every time.

    And would I appreciate anyone praying for me? I would of course appreciate the sentiment, but would not expect it to have any effect whatsoever on the outcome. Unlike science, prayer has no observable effect on the course of events in the real, physical world…which is, as far as I know, the only world there is.”

    Like most atheists- Al wants to claim that science and religion are two opposite ideas, they can’t come together, that religion is nonsense fantasy and science is the real world and common sense. Notice how there are only two choices- ‘science or religion’…I assume from his comments he doesn’t think you can have both.

    His mindset is probably why he never has anything of value to add to ANY discussion here.

  27. 27
    JasonTheGreek says:

    BTW- If you think I’m being harsh. Go back through the various posts Allen has commented in and check out his often hateful remarks towards Bill, Denyse, and the rest of us. Some of his comments were so hateful they were actually deleted. One should expect more from a college professor, let alone someone who claims to want to add to the debate in a civil and polite manner, yet shows the opposite in 90% of his comments.

    When someone else comes here and shows incivility and calls names, attacks with bogus straw men, they are quick to get the boot. And for good reason. If you can’t stop being arrogant and acting as if you’re up on high looking down upon all of us fools- you have nothing of value to add to the discussion period.

  28. 28

    Kairos wrote:

    “But 150 years ago they thought cells were a mere biological jello; as you know things are now MORE AND MORE worse for susch a sort of speculations.”

    Precisely; and how did we find out that cells were more than just bags of protoplasm? By doing a century and a half of intensive lab work, all of it originally stimulated by Darwin’s testable hypothesis. Was it IDers who figured out the constituents and operation of cells, or biologists, using the scientific method, as pioneered by Darwin?

  29. 29
    kairos says:

    Thanks PaV and Jason for your comments. Concerning Al I wonder why he should put himself out of the religious realm. In his last messages he has just shown his strong faith …

  30. 30
    kairos says:

    #30

    “Precisely; and how did we find out that cells were more than just bags of protoplasm? By doing a century and a half of intensive lab work, all of it originally stimulated by Darwin’s testable hypothesis. Was it IDers who figured out the constituents and operation of cells, or biologists, using the scientific method, as pioneered by Darwin?”

    Please don’t bluff. Darwin did not really influence how science in biology has been done. One thing is science, another darwinism

  31. 31
    mike1962 says:

    MacNeill: “So the real question is, are the “engines of variation” sufficient to produce the raw material upon which natural selection operates, producing the adaptations we see in living organisms? So far, based on what we have observed in studying living organisms (and the genetic and developmental mechanisms by which they change over time) the answer is yes.”

    So the engines of variation you speak of are sufficient for novel cell types, tissues, and body plans? Where has this been demonstrated empirically?

  32. 32
    Atom says:

    Allen, I am among those here who appreciate your posts and as PaV pointed out, to me you fight fair.

    I feel that the longer you stick around here, the more the lights will begin to click on. It is good to have your ideas challenged and you are up-front in admitting that past NDE mechanisms (RM+NS) have proven fruitless in producing the change necessary for Macroevolution to occur. You propose new mechanisms. Good. When you discover that these new mechanisms for adaptation are non-random and built-in responses, (i.e. complex systems that themselves need to be explained), perhaps you will be more comfortable tenatively holding to the Design hypothesis.

  33. 33
    mike1962 says:

    MacNeill: “Actually, we do. As just one example, we know that a fusion of two chromosomes in a primate ancestor in the hominid line is correlated with the divergence between the line that led to humans and the line that led to chimps and other great apes.”

    Correlated? That’s not an indication of causation any more than the presence of raincoats on my kids somehow indicating that raincoats cause rain. Sorry, sir, now you’re just being sloppy.

  34. 34
    Atom says:

    On the heels of my last comment…

    Allen:

    Was it IDers who figured out the constituents and operation of cells, or biologists, using the scientific method, as pioneered by Darwin?

    Notice how you contrast “IDer” with “Biologist using the scientific method”. You should know better than to claim that no true biologist would be an IDer.

  35. 35
    mike1962 says:

    Pav: “Do the “engines of variation” provide sufficient variation to move beyond microevolution to macroevolution.”

    PaV gets the cigar today.

  36. 36
    mike1962 says:

    Pav: “The problem to be solved, and the question to be answered, is: can NS, acting alone, bring about a “rearrangement” of the “genetic program” of a particular organism. I, for one, accept the “fact” of evolution (i.e., the fossil record), and I conditionally accept “common descent” (stochastic, versus continuous, descent has not been ruled out; but this is but a fine point), and I accept that there are many “mechanisms of variability”, but logically Darwinian evolution (i.e., variability, inheritance, fecundity) seems completely impotent in “stochastically” arriving at a new “program mode” for DNA/RNA information systems.”

    Well put PaV. Reading this sort of thing gives me tingles of joy, because it is on this front where all the action lies. I predict it’s going to be process control, and information theory types who will bring the next round of great gains here. Our bio system was come to be seem as a fantastically designed system “with the appearance of not being designed” on certain levels. The ultimate irony.

  37. 37
    PaV says:

    Allen MacNeil (in response to Joseph):
    Two quotes:

    First

    We don’t yet know whether or not variation coupled with inheritance, fecundity, and resulting in differential survival and reproduction has done this because we are still investigating such possibilities. That’s what science is all about: doing the hard work in the field and in the lab that either falsifies one’s hypotheses or not.

    Second quote:

    . . . evolutionary biologists will continue to assert (with a century and a half of empirical evidence to back them up) that ID “theories” (which to date are no more than hypotheses) have no empirical support, and are therefore not science.

    There seems to be a contradiction here. Either the 150 years of “empirical evidence” validates the “theory” or it doesn’t. If it has been validated, then this “theory” should be making predictions, which, in turn, are either confirmed or negated, leading to either a strengthening of the theory or an ultimate rejection of the theory.

    If you are now in the lab doing all this hard work to figure out “whether or not variation coupled with inheritance, fecundity, and resulting in differential survival and reproduction has done this”, then what are the “predictions” that are guiding your investigations? What, exactly, does Darwinism predict here? If you haven’t any, then “variation coupled with inheritance, fecundity, and … differential survival and reproduction” can never be falsified. So, please tell us, what is it you’re looking for.?

    While you’re mulling that over (as I stated when I posted this summary article) I “predicted” that junk-DNA would be found to be highly significant, and that it would be involved in the regulation of the coding (and the non-coding/binding ) portions of DNA, which is no more than what would be clearly expectated if one starts from a design perspective. These “predictions” have been borne out. But, as I posted a few days back, all of this is a “surprise” to Darwinists. This means, they are not only NOT “predicting” it, but flummoxed when they encounter it. So what good is this Darwinism that has a 150 years of proof, but which still is yet to be proven? If it can’t “predict” anything, while a competing theory is accurately “predicting”, then don’t you think it’s time for a change?

    And, BTW, there is “evidence” for ID. It’s called IC. Meanwhile, RM+NS, the savior–via the Modern Synthesis–of Darwinism, has now been cast aside. Yet, somehow, Darwinism lives on. How is that?

  38. 38
    PaV says:

    mike 1962:

    whether or not variation coupled with inheritance, fecundity, and resulting in differential survival and reproduction has done this because we are still investigating such possibilities.

    I would concur. I think we’ll be seeing more and more collaborative efforts between life science type and those working in the physical sciences, with all of this opening up the door for the guys in information science.

    As John Davison would say: “How I love it so!”

  39. 39
    PaV says:

    Allen MacNeil:
    “Was it IDers who figured out the constituents and operation of cells, or biologists, using the scientific method, as pioneered by Darwin? ”

    Allen, you make it sound like Darwin discovered the “scientific method”. I’m sure you don’t mean that.

    But since you’re talking about the “scientific method”, here’s what Roger Bacon has to say in the Novum Organum (in which he describes what we call as the “scientific method”):

    Lastly, there are others who appear anxious lest there should be something discovered in the investigation of nature to overthrow, or at least shake religion, particularly among the unlearned. The two last apprehensions appear to resemble animal instinct, as if men were diffident, in the bottom of their minds, and secret meditations, of the strength of religion, and the empire of faith over the senses; and therefore feared that some danger awaited them from an inquiry into nature. But any one who properly considers the subject, will find natural philosophy to be, after the word of God, the surest remedy against superstition, and the most approved support of faith. She [i.e., natural philosophy=science] is therefore rightly bestowed upon religion as a most faithful attendant, for the one exhibits the will and the other the power of God.

    Yes, that’s right, the “scientific method” is meant to serve “faith”, not eradicate it.

  40. 40
    Michaels7 says:

    Professor Allen stated,

    “As to the question of patents, as I pointed out in my original post, Nobel prizes are awarded for discoveries, not applications (with the exception of the prize for physiology or medicine, which is sometimes awarded to the development of new diagnostic or therapeutic techniques). Therefore, no matter how revolutionary or useful, a new technology such as the one developed by John Sanford will not warrant a Nobel prize. However, a new discovery, such as the 3 degree black body radiation discovered by accident by Penzias and Wilson won them a Nobel prize in physics, even though the full theoretical explanation for the discovery was done by others.”

    As I pointed out in my post. I put forth some sarcastic statements and then asked real questions about Modern Synthesis, EvoDevo, Cornerstone.

    You ignored the serious question and as I suspected you would answered the easy dunk.

    Will you not go on record to my real questions?

  41. 41
    Michaels7 says:

    Chris, Zachriel,

    Ty for response. I’ll respond to you both after Dr. MacNeill responds to my serious line of questions as you both did.

  42. 42
    DaveScot says:

    Allen MacNeil

    Your notion that nobel prizes are awarded for discoveries-only is all wet.

    (my emphasis)

    In physics:

    Awarded by the Royal Swedish Academy of Sciences to “the person who shall have made the most important discovery or invention within the field of physics”.

    In chemistry

    Awarded by the Royal Swedish Academy of Sciences to “the person who shall have made the most important chemical discovery or improvement“.

    You need to do less writing and more reading professor.

    For instance, check out all the prizes awarded for inventions in physics:

    http://en.wikipedia.org/wiki/N.....in_Physics

    One more thing of note, I couldn’t find a single noble prize award for any discoveries in evolutionary biology.

    Check out all these physiology/medicine awards.

    http://en.wikipedia.org/wiki/N.....r_Medicine

    All of them are directly or indirectly driven by the study of living tissue. Modern biology is the study of living tissue and is not dependent on how it got that way. How it got that way is historic biology. Historic biology appears to me to be about useful as teats on a tomcat.

    It appears you evolutionary biologists are just leeching off the discoveries and inventions made by chemists, physicists, and physiologists. When are you going to go out and do some real research that leads to the betterment of the human condition? 😆

  43. 43
    DaveScot says:

    Michaels7

    Here is the definitive way of identifying inventors who’ve been issued patents.

    http://patft.uspto.gov/netacgi.....038;d=PTXT

    No hits on “MacNeill; Allen”.

    Conversely if we check my name

    http://patft.uspto.gov/netacgi.....038;d=PTXT

    Four of the eleven hits on “Springer; David” are mine.

    So unless I spelled Allen’s name incorrectly or he goes by some other name he’s not a named inventor on any granted U.S. patent.

    As an aside, this invention of mine

    http://patft.uspto.gov/netacgi.....PN/5936608

    was inspired by my knowledge of human anatomy and physiology. It’s basically a method of conserving power in a certain type of flat panel display by figuring out what element(s) on the display screen are being focused upon by the eyes and gradually lowering the brightness (which reduces the power consumption) of all elements not in focus. The visual system in humans (and other higher animals) works the same way. Things in the central focus are processed in high resolution and those on the periphery in low resolution. That way the brain doesn’t get overloaded by applying an equal amount of processing power to the entire field of vision. The way color was added to black and white TV was similarly inspired. The color content in an NTSC video image is only about a fifth of the resolution of the black and white (brightness) content. That’s because the human eye is much more sensitive to brightness of light than it is to the frequency of the light. Knowing that, color content could be added onto the 14 megahertz amplitude modulated black/white carrier by the addition of a 3.5 megahertz phase modulated sub-carrier. In other words brightness is painted with a very fine brush and then color is slopped over the top with a much wider brush.

  44. 44
    kairos says:

    #44

    For instance, check out all the prizes awarded for inventions in physics:

    May I cite a name for all?
    Guglielmo Marconi

    It appears you evolutionary biologists are just leeching off the discoveries and inventions made by chemists, physicists, and physiologists. When are you going to go out and do some real research that leads to the betterment of the human condition? 😆

    Perhaps are we waiting Godot?

  45. 45
    kairos says:

    #39 Agree PaV

    While you’re mulling that over (as I stated when I posted this summary article) I “predicted” that junk-DNA would be found to be highly significant, and that it would be involved in the regulation of the coding (and the non-coding/binding ) portions of DNA, which is no more than what would be clearly expectated if one starts from a design perspective.

    But instead it’s very bad news for NDE. One of the reason NDEers have been able up to now to sell a minimal plausibility for RM+NS is by claiming that only a SMALL part of DNA is actually active. If this is not the case, mere statistics is sufficient to get NDE buried. And this without taking into account hierarchy and other complex features that could show DNA even more “designed”.

  46. 46

    DaveScot wrote:

    “I couldn’t find a single noble prize award for any discoveries in evolutionary biology.”

    The Nobel prize for physiology or medicine for 1973 was awarded to Konrad Lorenz, Niko Tinbergen, and Karl von Frisch for their work in founding the science of ethology, which is the science of animal behavior from an explicitly evolutionary perspective. My own field – evolutionary psychology – is a direct subdiscipline of ethology; that is, it is the ethology of humans.

  47. 47

    Kairos wrote:

    “…no engines of that sort are a plausible explication of life.”

    That’s true: the mechanism that Darwin proposed in 1859 (i.e. natural selection) was not proposed as an explanation of the origin of life. Indeed, Darwin did not propose any mechanism for the origin of life, nor did he speculate about it (beyond a single sentence fragment in the Origin of Species). As Daniel Dennett has shown, Darwin “started in the middle” by proposing a testable mechanism for descent with modification among organisms that already existed, and abjured speculation on the origin of life.

  48. 48

    Personally, I pay very little attention to the “origin of life” problem, as I believe that it is almost impossible to obtain evidence either way. Answering that question also should have little or no effect on answering the question, “once life exists and has a reliable mechanism for information coding and transfer, what happens?” The answer is, it evolves into what we see around us today.

  49. 49

    PaV asked:

    “Do the “engines of variation” provide sufficient variation to move beyond microevolution to macroevolution.”

    This is indeed the central question. One of the central tenets of the “modern synthesis of evolutionary biology” as celebrated in 1959 was the idea that macroevolution and microevolution were essentially the same process. That is, macroevolution was simply microevolution extrapolated over deep evolutionary time, using the same mechanisms and with essentially the same effects.

    A half century of research into macroevolution has shown that this is probably not the case. In particular, macroevolutionary events (such as the splitting of a single species into two or more, a process known as cladogenesis) do not necessarily take a long time at all. Indeed, in plants it can take as little as a single generation. We have observed the origin of new species of rose, primroses, trees, and all sorts of plants by genetic processes, such as allopolyploidy and autopolyploidy. Indeed, most of the cultivated roses so beloved of gardeners are new species of roses that originated spontaneously as the result of chromosomal rearrangements, which rose fanciers then exploited.

    The real problem, therefore, is explaining cladogenesis in animals. As Lynn Margulis has repeatedly pointed out, animals have a unique mechanism of sexual reproduction and development, one that apparently makes the kinds of chromosomal events that are common in plants very difficult in animals.

    However, she has proposed an alternative mechanism for cladogenesis in animals, based on the acquisition and fusion of genomes. Research into such mechanisms has only just begun, but has already been shown to explain the origin of eukaryotes via the fusion of disparate lines of prokaryotes, plus the origin of several species of animals and plants as the result of genome acquisition. As Lynn has been extraordinarily successful in the past in proposing testable mechanisms for macroevolutionary changes, I look forward to many more discoveries in this field.

  50. 50

    PaV also asked:

    “…can NS, acting alone, bring about a “rearrangement” of the “genetic program” of a particular organism?”

    As John Endler, Will Provine, and myself have repeatedly pointed out, natural selection can’t “bring about” anything. Natural selection isn’t a mechanism, it’s an outcome. The mechanisms that bring about natural selection are variation, inheritance, fecundity, and differential survival and reproduction.

    In other words, the rearrangement of the genetic program of a particular organism is not the result of natural selection, it is the result of one of the “engines of variation” to which I referred in one of my earlier comments. The ID strawman of “RM” (i.e. random mutation) is a pale shadow of these “engines,” about which we know surprisingly little, but about which we are learning an immense amount at present.

    And yes, it nows seems that something like what Richard Goldschmidt proposed as the basis for cladogenesis might not be so far-fetched at all. The idea of a single-step “hopeful monster” was not rejected by the founders of the “modern evolutionary synthesis” on empirical grounds, it was rejected because it could not be explained using the “one gene: one trait” model of genetics that was in vogue at the time.

    With the rise of evolutionary developmental biology (i.e. “evo-devo”), we are beginning to realize that large-scale, relatively rapid changes in overall phenotype are possible, and that they can be explained by changes in the regulation of “master control genes” (i.e. homeotic genes). Furthermore, these insights are now beginning to be applied to the patterns of cladistic change visible in the fossil record, as first forcefully pointed out by Eldredge and Gould in 1972.

    What is now happening, in other words, is that a new “evolutionary synthesis” is being formulated, based on a flood of new information from genetics, developmental biology, paleontology, and historical geology/planetology. This new synthesis takes into account new information that has been obtained since the heyday of the “modern synthesis” and provides a much more powerful and comprehensive explanation of Darwin’s “descent with modification.” No, it doesn’t rely completely on Darwin’s proposed “mechanism” of natural selection, at least not as formulated by Fisher/Haldane/Wright/Dobzhansky/Mayr, but yes it does conform to the overall outlines of Darwin’s original theory.

    So, as I said before, “the modern synthesis is dead; long live evolutionary biology!”

  51. 51

    Mike 1962 asked:

    “So the engines of variation you speak of are sufficient for novel cell types, tissues, and body plans? Where has this been demonstrated empirically”

    Yes; you can read all about it in Sean Carroll’s new book Endless Forms Most Beautiful and in Lynn Margulis’s classic Symbiosis in Cell Evolution and her more recent Acquiring Genomes, coauthored with her son, Dorion Sagan (yes, that Sagan; Lynn was Carl’s first wife).

  52. 52

    Mike 1962 wrote:

    “I accept that there are many “mechanisms of variability”, but logically Darwinian evolution (i.e., variability, inheritance, fecundity) seems completely impotent in “stochastically” arriving at a new “program mode” for DNA/RNA information systems.””

    Actually, that’s exactly what homeotic gene regulatory mechanisms are eminently capable of. And as to “stochastically” arriving at a new “program mode”, that is precisely what differential survival and reproduction is: a stochastic mechanism by which new variations are sorted and tested against the environment, which ultimately “chooses” the most efficient variation out of those produced by the “engines of variation.” Not to put too fine a point on it, but this is just Darwin’s theory of evolution by natural selection, restated in terms of “information theory.”

  53. 53

    I sense some confusion about the term “stochastic” in some of the previous comments. the term is usually used to refer to any process that includes a random component (see http://www.m-w.com/cgi-bin/dic.....stochastic ). It does not mean “happening in a discontinuous manner,” as some commentators seem to imply. This distinction is extremely important, as evolution is indeed a stochastic process; it includes both a random component (i.e. many of the “engines of variation” generate apparently random variations) and a non-random component (i.e. differential survival and reproduction, as specified by the environment). Nothing in Darwin’s original theory of evolution required that “descent with modification” be absolutely continuous. True, Darwin used the latin phrase “natura non facit saltum” several times, but the diagram that he included in the Origin (the only illustration in the book) shows a branching process of cladogenesis not substantially different from that proposed by Eldredge and Gould in 1972.

    In other words, there is nothing about the concept of naturalistic evolution that requires that it be a continuous, gradualistic process. The fossil record as we now understand tends to support the idea that macroevolution is relatively discontinuous, with relatively long periods of “stasis” punctuated by relatively brief periods of cladogenesis, usually correlated with either mass extinction/adaptive radiation events, founder effects/bottlenecks, and/or genetic innovations such as the fusion of prokaryotes into the eukaryotic endosymbiont. In other words, microevolution (i.e. natural selection, genetic drift, and other processes that happen anagenetically at the population level) and macroevolution (i.e. extinction/adaptive radiation, genetic innovation, and symbiosis that happen cladogenetically at the species level and above) are in many ways fundamentally different processes with fundamentally different mechanisms. Furthermore, for reasons beyond the scope of this thread, macroevolution is probably not mathematically modelable in the way that microevolution has historically been.

    I am just beginning work on a book on macroevolution in which I intend to develop these ideas much more fully. However, as I am already working on an introductory evolution textbook for non-scientists and a lecture series on evolutionary psychology for the Teaching Company, not to mention an ongoing research project on the evolutionary dynamics of vertical polygamy in America and a book on the evolution of the capacity for religious experience for a major university press, it will probably not be finished for several years.

  54. 54

    P.S. DaveScot:

    Congratulations on all your patents. I don’t work in a field in which patents are either likely or possible (most research scientists don’t). However, you might be interested in reading my most recent publication: chapter 10 (“The Capacity for Religious Experience is an Evolutionary Adaptation to Warfare”) in Fitduff, M. & Stout, C. eds. (2005) The Psychology of Resolving Global Conflicts, vol. 1, Praeger International Series, Westport, CT. This is a slight revision of a paper that appeared in vol. 10 #1 (July 2004) of Evolution & Cognition, published by the Max Plank Institute in Vienna. I would be happy to email you a pdf of either document, or you can read about them at my blog:
    http://evolutionlist.blogspot......ce-is.html

  55. 55
    Joseph says:

    Joseph asked:

    “…why don’t we know what mutations afforded what changes? ”

    Allen MacNeil:
    Actually, we do. As just one example, we know that a fusion of two chromosomes in a primate ancestor in the hominid line is correlated with the divergence between the line that led to humans and the line that led to chimps and other great apes. We know this because human chromosome #2 is the product of this fusion, a conclusion that is based on pure empirical genetic testing.

    Umm, you didn’t say what changes the alleged fusion afforded. And I have had discussions with a Scott Page of Norwich U who tells me that no one thinks the event you mention had any significance at all- and his specialty is primates.

    We still don’t know what mutations allowed for upright, bipedal motion.

    Joseph also asked:

    “Why don’t we even know whether or not ANY mutation/ selection process can account for the range of change required for Common Descent to be indicative of reality?”

    Allem MacNeil:
    We don’t yet know whether or not variation coupled with inheritance, fecundity, and resulting in differential survival and reproduction has done this because we are still investigating such possibilities. That’s what science is all about: doing the hard work in the field and in the lab that either falsifies one’s hypotheses or not.

    If we don’t know then that is what should be presented to students. To keep pushing that we do know or that we will know in time is just plain hypricritical.

    Everything in the field and lab points to wobbling stability.

    Allen MacNeil:
    Referring to CSI, IC, and other ID ideas isn’t doing science at all. It does not involve doing actual experiments or field observations, it simply relies upon conceptual arguements, arguments that so far have no empirical support.

    Actually CSI, IC and counterflow all have been observed in the lab and in nature. All can be tested against their respective definitions. And it should also be noted that there are some anti-IDists who have (falsely) claimed to have refuted the concept of IC via experimentation. That fact alone contradicts your response.

    Allen MacNeil:
    Until IDers start performing actual experiments or gathering field data that clearly and unambiguously distinguish between EB and ID hypotheses, evolutionary biologists will continue to assert (with a century and a half of empirical evidence to back them up) that ID “theories” (which to date are no more than hypotheses) have no empirical support, and are therefore not science.

    And again by YOUR criterion EB isn’t science either. There aren’t any experiments which demonstrtae a population of ape-like organisms can “evolve” into a population of humans. Only a handful of wishful speculations based on the assumption such a thing did occur.
    ———————————————————

    Allen MacNeil:
    Personally, I pay very little attention to the “origin of life” problem, as I believe that it is almost impossible to obtain evidence either way. Answering that question also should have little or no effect on answering the question, “once life exists and has a reliable mechanism for information coding and transfer, what happens?” The answer is, it evolves into what we see around us today.

    Try this Allen:

    If living organisms did NOT arise from non-living matter via stochastic mechansims there would be no reason to infer the subsequent diversity arose solely via those types of processes.

    IOW the origins of living organisms directly impacts any subsequent evolution.

  56. 56
    DaveScot says:

    Allen

    I read the 1973 Physiology Nobel acceptance speech and aside from a passing reference to natural selection in the first paragraph, which appears completely gratuitous (as most such references are when the actual discovery was accomplished through the study of living tissue), I could find no other mention of evolution. Moreover, even if you argue the mention wasn’t gratuitous it makes no mention of chance mutation being the source of variation which natural selection acts upon. I really only have a problem with the exclusion of telic mechanisms not with natural selection acting to filter the good from the not good in direct response to the environment. In other words, my problem isn’t in survival of fitness but arrival of fitness.

    http://nobelprize.org/nobel_pr.....peech.html

    As an aside, in reading Lorenz’ biography he talked about the importance of birds in his studies. I’ve raised a lot of different birds from nestlings and found they instinctively do a lot of birdlike things without ever being around another bird. Like flying. It seems rather farfetched to imagine a protein cascade of some sort that accounts for a bird instinctively knowing how to fly or how to build a nest characteristic of its species (location, building materials, and construction details) yet they do. Obviously the nest building instructions are contained in the egg. How? My first guess would be it’s somehow encoded in the “junk” DNA.

  57. 57
    DaveScot says:

    Allen

    Patents became a lot more common in my field in the 90’s although part of that with me was working for small companies where trade secrets were the rule and patents were the exception. I really only patented a few things at Dell because it was a requirement in my performance plan to generate patents. And even then the only reason we did it as a company was because IBM and Texas Instruments was taking us to the cleaners in broad patent license fees. It’s a racket. Big companies with big patent portfolios threaten small companies with expensive litigation then settle for annual license fees that grant immunity from infringement. IBM alone was clocking us for over $100 million annually. That was a huge chunk of our profits. Around 1998 we developed a big enough portfolio of our own (and enough money to pay lawyers to sue IBM for infringement) so that we could broker a cross-license deal (we don’t sue you, you don’t sue us) and get out from under that annual extor… er, I mean, license fee. Many of us down in the trenches doing the inventing feel the same way as many idealistic academics – discoveries should be made public for everyone to use freely. That’s why there’s so much public domain software nowadays. In my field there’s a lot of crap patents that should never have been granted too (as I suppose in yours there’s a lot of crap papers that should never have been published). The reason I suspect is the same – poor peer review. Patent examiners (our equivalent to peer review) have little knowledge of prior art unless the prior art was patented. Things that are commonly done by experts in the field or were poorly kept trade secrets receive patents all the time because the examiners don’t know they aren’t novel. And once a patent is issued the burden of proof is on the accused infringer in court to defend himself as the assumption is that the patent examiners did their job well. Like I said, it’s a racket, but what can you do? “Publish or perish” has an analog in my field: “Patent or perish”.

  58. 58
    DaveScot says:

    Allen

    re religion conferring survival advantage

    Chance & necessity is able to explain an awful lot of things after the fact but has very little predictive power. It’s tough predicting what random variation will produce. I’d be really impressed if evolution predicted religion before religion was there or if it could predict what path religion was going to take in the future or when & where religion will arise in another animal species. Of what practical use is a theory which only explains things after the thing is actually observed and is so flexible that practically any observation can be explained by it? Altruism is a good example. Evolution explains both the lack of it and the manifestation of it. It never predicts where it will be found it only explains how it happened after it is found (or not found). Then for the few things it can’t explain we get a Darwin of the Gaps defense in that evolution must have done it we just don’t know how yet (queue the flagellum). Either that or the theory is modified ad hoc to accomodate observations that don’t fit (queue up punc eek). Or bits of it are discarded with no widely publicized admission of how badly wrong it was (queue up gene-centric theory). I know you stand out from the herd in that you’re willing to say the modern synthesis is dead or dying but you might want to consider that its death was a prediction of ID going back at least to Paley. I’ll further predict that you’ll never find a theory of everything in biology (which must include the origin of life as well as its diversification) that survives for the long haul if it excludes intelligent agency as a mechanism. In other words, you can search for a blind watchmaker until the cows come home and you won’t find one. The reason is simple – you can’t find that which does not exist. There’s no such thing as a blind watchmaker.

  59. 59
    PaV says:

    Allen MacNeil:

    Here are two quotes taken from two different posts on this thread:

    According to Darwin, natural selection is the inevitable result of three pre-conditions: variation, inheritance, and fecundity. Given these three pre-conditions, some individuals survive and reproduce more often than others. As a result, their heritable variations become relatively more common over time in the populations of which they are members.

    In other words, the rearrangement of the genetic program of a particular organism is not the result of natural selection, it is the result of one of the “engines of variation” to which I referred in one of my earlier comments.

    There’s a tremendous ambiguity produced by these two statements. In the first, you postulate NS acting on the end-product of variation, inheritance and fecundity (by which, I’ll presume, you mean that the “mutant” can reproduce), while in the second you attribute tremendous change to the “engines of variation”, leaving NS completely out of the picture. The only way to reconcile these two statements is to say that nature produces “hopeful monsters”, and some of them live, which, then, makes NS completely moot. This almost has the appearance of saying that when it is convenient to talk about NS doing something, then we’ll talk about it. But if it isn’t convenient, then we’ll just leave it out and talk about “variation”. In this case, the “rearrangement of the genetic program” occurs through the “engines of variation”, and NS has nothing to do with it. But, of course, this sounds exactly like what Goldschmidt was saying in 1940, only, not knowing about DNA as we do, he talked about chromsomal rearrangments bringing about “systemic mutations”–an alteration in how the program of development takes place.

    Now the wonder of all of this is that we are always told that evolution is not a “chance process”, because NS in some way “confines”, let us say, these chance events. But here you are saying we have “chance events” which modify a genetic program, so it’s a completely “stochastic’ event. If Darwin insists–as he did–that “natura non facit saltum”, then he’s proven wrong. Why should his theory stand?

    The ID strawman of “RM” (i.e. random mutation) is a pale shadow of these “engines,” about which we know surprisingly little, but about which we are learning an immense amount at present.

    I don’t think it entirely fair that RM is ID’s “strawman”. This blog has countless posters who invoke RM +NS as the cause of evolution. But, in the second quote above, in answering the question about the “reprogramming of genetic programs”, you’re intimating that some “random mutation”, whether it be an insertion, deletion, crossover, or even point mutation, has affected a Hox gene with a resultant “change” in how the developmental program unfurls. I was pointing that out above. So, I don’t really see it as a “strawman”. I suspect it’s just simply something you don’t want to spend time defending, which I well understand.

  60. 60

    DaveScot wrote:

    “Altruism is a good example. Evolution explains both the lack of it and the manifestation of it. It never predicts where it will be found it only explains how it happened after it is found (or not found).”

    Actually, W. D. Hamilton’s theory of kin selection predicts exactly where altruism resulting from kin selection should be found: in the order Hypmenoptera (ants, bees, and wasps). And, sure enough, almost all of the cases of intense eusociality have evolved within that order. Hamilton based his prediction on the sex determination mechanism in Hymenoptera: females are normal diploids, but males are haploid. This means that sisters (i.e. the workers and the queen in a hive) are related to each other by more than they would be to their own offspring (three-fourths versus one-half), and therefore those females who assist one of their number (the queen) in reproducing actually cause more copies of their genes to be replicated in the next generation than they would if they themselves passed them on.

    Since Hamilton made his prediction, it has been exhaustively tested, not only in insects but also in birds, mammals, fish, reptiles, and a myriad of other animals. In virtually every case, his prediction has turned out to be accurate: the closer the genetic relationships between a group of animals, the more likely they are to act altruistically toward each other. Indeed, such correlations are so common and so predictable, Hamilton’s hypothesis is now often refered to as “Hamilton’s Law.”

    What is interesting is that extreme cases of eusociality have also been observed in animals that do not use haplodiploidy for sex determination the way the Hymenoptera do. And, some of the Hymenoptera are not eusocial (the Ichneumonidae are a classic example). So, what Hamilton’s Law predicts is not an absolute rule, but rather a strong correlation (based on ecology and life history, as well as genetic relatedness).

  61. 61

    An interesting thought experiment also suggests itself, vis-a-vis the previous post. If haplodiploidy does NOT predispose the Hymenoptera to the evolution of eusociality, then why exactly are so many eusocial species found in that order? And why should unambiguous cases of relatively intense sociality be correlated with genetic relatedness in other orders, classes, and even phyla of animals?

  62. 62
    JFD says:

    Dr. MacNeill,

    DaveScot wrote;

    “Altruism is a good example. Evolution explains both the lack of it and the manifestation of it. It never predicts where it will be found it only explains how it happened after it is found (or not found).”

    And then Dr. MacNeill said;

    “Actually, W. D. Hamilton’s theory of kin selection predicts exactly where altruism resulting from kin selection should be found: in the order Hypmenoptera (ants, bees, and wasps). And, sure enough, almost all of the cases of intense eusociality have evolved within that order. ”

    So since you are answering DaveScot’s assertion that evolution explains but never predicts. Then Mr. Hamilton did not know the type of society that bee’s, wasps and ants had before he made this prediction in his theory. I find that hard to believe but maybe I missed DaveScot’s point.

  63. 63

    No, actually you missed the point of my post. Not all ants, bees, and wasps are eusocial. However, eusociality has evolved independently almost a dozen times in the order Hymenoptera, but only once in any other order of insects (the Isoptera) and only once in the entire subphylum Vertebrata (naked mole rats). In other words, Hamilton’s Law brilliantly predicts the evolution of eusociality as the result of a seemingly unrelated phenomenon: the mechanism of sex determination in Hymenoptera, which almost certainly evolved as a method for females to adjust the sex ratio of their offspring to respond to changes in their environment.

  64. 64
    j says:

    Allen MacNeill (49): “Indeed, Darwin did not propose any mechanism for the origin of life, nor did he speculate about it (beyond a single sentence fragment in the Origin of Species ).”

    Charles Darwin (1871, in Life and Letters of Charles Darwin):

    It is often said that all the conditions for the first production of a living organism are now present, which could ever have been present. But if (and oh! what a big if!) we could conceive in some warm little pond, with all sorts of ammonia and phosphoric salts, lights, heat, electricity, etc. present, that a protein compound was chemically formed ready to undergo still more complex changes, at the present day such matter would be instantly devoured or absorbed, which would not have been the case before living creatures were formed.

    Making false claims about what Darwin wrote is getting to be a habit of yours, Dr. MacNeill. (Cf. http://www.uncommondescent.com/archives/1714 comments #38 and #45.)

    Per DaveScot (44): “You need to do less writing and more reading professor.”

  65. 65
    JasonTheGreek says:

    An accidental mechanism evolved (without plan or purpose) to provide a purposeful method of ADJUSTING sex ratio?

    Sounds quite teleological to me.

  66. 66

    Backing away from true eusociality, Hamilton’s Law has been used to find less extreme versions of kin selection in animals as diverse as ground squirrels, scrub jays, and (surprise!) primates. Indeed, as biologists look for additional applications of Hamilton’s Law, we find them in multiple locations, often right out there where we could have seen them all along, but didn’t until we had Hamilton’s Law to point the way.

    That is how real science works: an hypothesis is proposed, used to make predictions, which are tested in the field and in the lab, and the results compared with the original hypothesis. In the case of Hamilton’s brilliant insight, his hypothesis has been so thoroughly tested and its applications so fruitful in our understanding of animal social behavior that it deserves at least the appellation of “theory” and, in time, will almost certainly be acclaimed as a scientific “law.”

  67. 67
    JasonTheGreek says:

    Don’t worry J- one could always argue that random in science sonehow doesn’t mean the same thing in everyday language…and that words like ‘accidental’ and ‘purposeless’ mean something different in science as well.

    Darwinist: “They don’t really mean a lack of purpose or intent or that the event was accidental- science can’t answer questions like these! That’s philosophy.”

  68. 68

    j asserts that Darwin speculated on the origin of life with his “warm little pond” quote. However, that quote is taken from a letter that Darwin wrote to another naturalist and was never published in book form, either during his lifetime or thereafter. It is, of course, collected in his correspondence.

    Try this: find a quote in Darwin’s published works (i.e. those he published during his lifetime) in which he speculates as to the origin of life. And please note that I have already mentioned the sentence fragment from the last paragraph of the Origin, so that one is already off the table.

  69. 69
    JasonTheGreek says:

    Is anyone else tired of every comment from Al containing something to this effect:

    “ID isn’t real science”
    “_____INSERT IDer NAME isn’t a real scientist”
    “IDers refuse to do lab work, aka real science”
    “That is how real science works”

    Maybe I’m alone, but it’s like listening to a broken record.

  70. 70
    JasonTheGreek says:

    Allen. Are you kidding?

    You said:

    Allen MacNeill (49): “Indeed, Darwin did not propose any mechanism for the origin of life, nor did he speculate about it (beyond a single sentence fragment in the Origin of Species ).”

    J provides a full paragraph. You argue that it wasn’t published in his lifetime. So, if you make a speculation in WRITING, but it’s not “published” does that mean you never spoke on the issue?

    This is getting old fast.

    You never said “Darwin never spoke of OOL in PUBLISHED work. You said he never proposed any mechanism for the origin of life (period).” Add cavaets all you want. You were wrong. Be the gentleman you constantly claim to be….make a reference to how you’re an avid fencer and move along.

  71. 71
    JasonTheGreek says:

    By the way. J NEVER claimed that the quote from Darwin was in published print form when he was alive. He simply stated that Darwin DID propose an idea on the origins of life, which you said he did not.

  72. 72
  73. 73

    Indeed, as the following quote indicates, Darwin was uncomfortable with the whole idea of speculating on the origin of life:

    “But I have long regretted that I truckled to public opinion, and used the Pentateuchal term of creation, by which I really meant “appeared” by some wholly unknown process. It is mere rubbish, thinking at present of the origin of life; one might as well think of the origin of matter.”

    From a letter to J. D. Hooker, dated April 17, 1863. See:
    http://darwin-online.org.uk/co.....pageseq=30

  74. 74

    I speculate on a lot of things, sometimes in letters, sometimes in conversations, and often when thinking to myself, but none of those speculations amount to much if I don’t publish them. And, even then, they don’t amount to anything unless I (or someone else) attempts to verify if such speculations are, in fact, supported by empirical evidence.

    So, I amend my earlier assertion thusly: Darwin did not speculate on the subject of the origin of life in any publication during his lifetime, and as the later quotation I provided above indicates, he regretted ever having done so at all, and believed that the subject was as far beyond the reach of science as speculation about the origin of matter itself.

    And I agree with him.

  75. 75

    And now gentlemen, if you will excuse me, I have a lecture on evolution to prepare for tomorrow. It’s been grand!

  76. 76
    JasonTheGreek says:

    Good. Now, I know how it works. I can make any statement, no matter how false. Then just come back and say I ammend my false statement to add a caveat to it and all is fine and well. Darwin’s thoughts on the origin of life shouldn’t be taken into consideration, because they weren’t published, and because he, at a later date, decided it probably wasn’t a good idea to speculate on the subject.

    Wow. I knew academia in the US was pretty messed up, but who knew it got this absurd?

  77. 77

    Jason, I refuse to engage with you further, on any subject.

  78. 78

    Interesting: twice now I have posted a quotation from Darwin clearly indicating that he regretted ever speculating on the origin of life, and twice it has disappeared.

  79. 79

    Perhaps it’s because it contains a weblink to the quotation, which is to be found at John Whye’s website, “The Collected Works of Charles Darwin.” The quotation is in a letter Darwin wrote to Joseph Hooker in April of 1863. You can probably find it yourself using the search box at Whye’s website.

  80. 80

    Here, at least, is the quote:

    “But I have long regretted that I truckled to public opinion, and used the Pentateuchal term of creation, by which I really meant “appeared” by some wholly unknown process. It is mere rubbish, thinking at present of the origin of life; one might as well think of the origin of matter.”

    C. Darwin to J. D. Hooker.

    Down, Friday night [April 17, 1863].

  81. 81

    Touché, et parry et riposte, non?

  82. 82

    P.S. Academics at Cornell are so “messed up” that I have twice been nominated for the Clark Award for outstanding teaching to undergraduates (nominated by my students, I might add). Maybe they know something you don’t, eh?

  83. 83
    Joseph says:

    Who cares what Darwin said?

    Try this Allen:

    If living organisms did NOT arise from non-living matter via stochastic mechansims there would be no reason to infer the subsequent diversity arose solely via those types of processes.

    IOW the origins of living organisms directly impacts any subsequent evolution.

  84. 84

    Have a grand week, folks – au revoir!

  85. 85
    JasonTheGreek says:

    Yes. Al. Don’t engage me, because I point out your incivility and your refusal to be totally honest.

    I do so apologize.

    Btw…

    Wow. (I say “wow”, because if you follow politics, you probably know Rockwell is considered far far out there by most.) If you google Al’s name, this is on the first page.

    http://www.lewrockwell.com/orig7/macneill1.html

    The point of posting this?

    It fits the pattern of political worldviews and ID and related ideas. Liberal-minded folk seem to hate ID more often than that…and conservatives are most often friendly to the idea. Rockwell, by the way, is almost surely out of his mind if you follow politics he’s a guy that will come up every now and again.

    Has anyone else noticed this? It seems liberals so often are disgusted by the very thought of allowing ID a seat at ANY table. Weird considering liberal-minded people should be all about letting all voices be heard.

    I wonder if this topic has been written about before. The apparent link to political worldviews and the refusal to even LISTEN to ID arguments?

  86. 86
    JasonTheGreek says:

    Also. My point, Al, was that you were 1. dishonest, and 2. basically called J a liar then refused to apologize when you were proven wrong with your assertion.

    Shall I remind everyone how you called OLeary abd Dembski immoral cretins who lack any moral fiber whatsoever in that post a few months ago? Or maybe I can paste your comment where you attacked ALL of us who post to this site in support of ID?

    You’re a disgrace as a teacher and a so-called gentleman, so please don’t worry. I’d rather not have anything to do with you, let alone engage you on any issue.

  87. 87
    kairos says:

    #49, 50

    “…no engines of that sort are a plausible explication of life.”

    That’s true: the mechanism that Darwin proposed in 1859 (i.e. natural selection) was not proposed as an explanation of the origin of life. Indeed, Darwin did not propose any mechanism for the origin of life, nor did he speculate about it (beyond a single sentence fragment in the Origin of Species). As Daniel Dennett has shown, Darwin “started in the middle” by proposing a testable mechanism for descent with modification among organisms that already existed, and abjured speculation on the origin of life.

    Al, I wrote “explication of life” not “origin of life”, so meaning the whole path to reach the past and actual life complexity. This requires obviously origin of life from inrganic matter but not only that, In this sense is perfectly worth ask if RM+NS could really do what NDEers claim. Up to now you have only supported tis claim with a typical (and useless) circular reasoning.

    Personally, I pay very little attention to the “origin of life” problem, as I believe that it is almost impossible to obtain evidence either way. Answering that question also should have little or no effect on answering the question, “once life exists and has a reliable mechanism for information coding and transfer, what happens?” The answer is, it evolves into what we see around us today.

    This is pretty wishful thinking which is done by presetting as possible just what it should be scientifically proved (Al, is this science?).
    Anyway I wonder how you can reasonably “pay very little attention to the origin of life problem” when this is the necessary step to allow furthr speculations about the mechanisms of evolution. Please excuse me but at least Francis Crick had a far more thoughtful approach to the problem.

  88. 88
    kairos says:

    #88 Jason I can understand but I cannot agree with your position. Although it is true that many NDE supporters are very rough against ID and are used to adopt rough”ad hominem” attacks I strongly think that:

    1. Actually this behavior shows how they are worrying that ID ideas could eventually modify the status of science as a mere materialistic state of affairs.
    2. The best thing to do is to be calm, to ask the “right questions” and to pretend answers for them.

  89. 89
    DaveScot says:

    Allen

    P.S. Academics at Cornell are so “messed up” that I have twice been nominated for the Clark Award for outstanding teaching to undergraduates (nominated by my students, I might add). Maybe they know something you don’t, eh?

    Oh yes, 20 year-olds are famous for their discriminatory powers. After all, they’ve experienced so much of life by that age, naive infatuations are something they just don’t fall for anymore, having left such things behind in their teens. 😛

    Here’s the link to the Darwin quote. I have no idea why it wouldn’t post for you except to think there was some blacklisted word that got it marked as spam included with the link.

    http://darwin-online.org.uk/co.....pageseq=30

    I note you are leaving us to prepare a lecture on evolution. Funny, I’d have thought you already would have had a lecture on that topic prepared by now.

    Oh hold it, it’s probably been a week since you last delivered a lecture on evolution and because it’s a narrati… er, I mean a theory in a constant state of flux you have to update it for last week’s ad hoc deletions and insertions. The evolution kludge du jour. I understand now.

    By the way Cornell is a great school. I grew up nearby. At some point I plan on moving back to the area. I was thinking about buying a small town nearby to rename in my honor and also start my own Christian ministry, focused of course on the study of why ID is a superior explanation for the origin and diversity of life and also why atheists lead intrinsically amoral lives. I’d let cash-strapped college students have a free place to live in my town in exchange for working part time in the ministry and evangelizing our precepts on campus. The best part is it’s all tax exempt. Hovind had the right idea but the wrong accountants. Good plan, eh?

  90. 90
    j says:

    Allen_MacNeill (Nov 12th 2006 at 9:40 pm): “Indeed, as the following quote indicates, Darwin was uncomfortable with the whole idea of speculating on the origin of life:

    But I have long regretted that I truckled to public opinion, and used the Pentateuchal term of creation, by which I really meant “appeared” by some wholly unknown process. It is mere rubbish, thinking at present of the origin of life; one might as well think of the origin of matter.

    From a letter to J. D. Hooker, dated April 17, 1863.”

    and

    Allen_MacNeill (Nov 12th 2006 at 9:44 pm): “…as the later quotation I provided above indicates, he regretted ever having done so at all, and believed that the subject was as far beyond the reach of science as speculation about the origin of matter itself.”

    You’re confused, Dr. MacNeill. The quote you provided was from 1863. By 1871, when he speculated about the “warm little pond”, he had obviously changed his opinion. Indeed, in Life and Letters of Charles Darwin, his son Francis (the volume’s editor) used the 1871 quote to properly offset the 1863 quote, presumably lest anyone get the wrong ideas about what his father thought about OOL).

    I find it amusing that you tried to use a quote from an unpublished (during his lifetime) letter against my use of a quote from an unpublished (during his lifetime) letter.

    BTW, thanks, Jason.

  91. 91
    Michaels7 says:

    DaveScott,

    Thanks for the follow up in rebuttal to Allen. But my real point was to issue a strawman to his strawman.

    He accuses others of the same argumentative jabs he makes.

    Nobel Prize, Patents, truth is different people with differen world views will win and make inventions.
    I just wanted to show how silly it was to throw out such an argument. As to the majority of beliefs during one era in time, it changes. It may start to change back again. Of course, the committee itself would need to possibly be replaced. They do nothing but make the most extreme political statements.

    Notice he has refused to answer my other questions related to EvoDevo, Modern Synthesis and Cornerstone of Evolution, Four Gene Types.

    He mentioned “this is the way he will teach it now”.

    Professor Macneill, can you answer my original questions with regards to the inconsistency within Evolution?

    Is Modern Synthesis truly superceeded? I pointed to PZ in order to show you that I see inconsistency within your own field.

    I find it interesting what children are learning today and what is actually being understood at the highest levels. It appears to me what you have is a sequential list of failing hypothesis, one right after another.

    I’m just asking to have a clear opinion from you.

  92. 92
    Patrick says:

    Allen,

    Has the old paradigm really been superseded as effectively as you claim? You may talk about “ID strawmen” and then discuss the ideas of yourself, Will Provine, Lynn Margulis, etc. as if they have become the majority but both Lynn and Will seemed to have received a lukewarm response at the fairly recent World Summit on Evolution. Has opinion swayed that much since that time or should you be more careful about what positions you label as strawmen? I’m curious to know the group consensus at this point…or does anyone know?

    You also seemed to have missed my earlier question:

    Alan, would you lend your name to support finding funding for additional ID research? I’m sure you believe that line of research will likely turn up fruitless in the end but I think you’d agree it’s at least worth the time to investigate with seriously funded research.

    Dave:

    One more thing of note, I couldn’t find a single noble prize award for any discoveries in evolutionary biology.

    The work of Ilya Prigogine could arguably be considered in support of evolutionary biology. Prigogine received the Nobel Prize for Chemistry in 1977 for his theory of dissipative structures. Although it has more to do with the origins of life…

  93. 93
    tb says:

    I think I know where his arrogance comes from!

    “a direct lineal descendant of Niall of the Nine Hostages, first high king of Ireland.”

    From:
    http://www.lewrockwell.com/orig7/macneill1.html

  94. 94
    DaveScot says:

    A zen buddhist, quaker, fencing enthusiast, libertarian, and last but not least a true Scotsman. And where does he choose to live… New York State, the most heavily taxed, socialistic, gun-grabbing, entitlement giving, big government state in the union. Chosen home of the Clintonistas for just those reasons.

    Non sequitur.

    The motto on my family coat of arms is

    Non mihi sed patriae.

    Translated: Not for myself, but for my country.

    It’s British. Allen’s attitude handily explains why there was a British Empire but no Scottish Empire, eh? 😛

  95. 95
    Michaels7 says:

    A Rose by any other name…

    I wonder if the experiments Dr. MacNeill point to with roses allow for rehybridization to go full circle. Much like Sunflowers?

    It appears Allen is out for the week. And I will not get an answer.

    Some conclusions he has reached should make Creationist very happy.

  96. 96
    DaveScot says:

    Awe darn. The charateristically wrong peanut gallery at ATBC including the recently banned Zachriel are taking exception to my saying that there was a British Empire but no Scottish Empire arguing that Britain includes Scotland.

    BZZZZZZZZZZZZZZZZT! Wrong. Scotland and England were not united until 1707 and the British Empire (technically the English Empire) at that point was already well on its way. Putting Scotland under the thumb of the English parliament in London was simply part of England’s expansion; another notch on the British belt.

    Adding insult to injury, there WAS an attempt by Scotland prior to 1707 to establish a Scottish Empire and it failed miserably.

    Scottish role

    There were several pre-union attempts at creating a Scottish overseas empire, with various Scottish settlements in North and South America. Nova Scotia was perhaps Scotland’s greatest opportunity at establishing a permanent presence in the Americas, but its most infamous was the ill fated Darién scheme which attempted to establish a settlement colony and trading post in Panama to foster trade between Scotland and the Far East.

    Further reading: The Complete Guide To The Scottish Empire

  97. 97

    […] MacNeill, Allen, in a comment on “We is Junk” article by PaV at Uncommon Descent, November 10, […]

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    […] MacNeill, Allen, in a comment on “We is Junk” article by PaV at Uncommon Descent, November 10, […]

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    […] with fundamentally different mechanisms,” as Cornell evolutionary biologist Allen MacNeill puts it. Who is […]

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    […] MacNeill, Allen. comment on “We is Junk” article by PaV at Uncommon Descent, […]

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