--------------------------------------------------------------------------------
Re: Now for phase II
--------------------------------------------------------------------------------
Hi Phospho,
I see this thread is getting extremely long and it becoming difficult to follow the various conversations others are having with you so I will focus only on posts I have addressed to you and you to me to simplify our interaction.
Regarding your question about accessing the journal materials, the only way you can access the journals via the web is if your library has an online subscription. I would ask at the front desk if they get Nature and Science online and I will do my best to only refer to articles that are commonly available though it may not always be possible. In those cases I will summarize the authors conclusions and how they arrived at them....let me know if this is ok for you.
Second, thank you for admitting that you have not had a biology education. I do not take issue with that but do take issue with you making definitive pronouncements about what science and scientists do i.e. you entire conspiratorial view of molecular biologists trying to promote false definitions of life on others as a practice....I will let you in on a little secret...about 99% of scientists don't give a damn about the public view of their work or have a desire to interact with the public the way I do, Taz does, SLPx does (if I am missing any other practicing scientist please feel free to rip into me .
Now to your post:
PLG: If I am understanding you correctly, you are talling about a neutral substitution, correct? In which case, it has no effect, and therefore I have no argument against this. My argument is against mutations that do have an affect.
M: But you do have an argument against this. You originally stood by the concept that ALL mutations are deleterios....the real FACT is that most mutations are neutral or slightly deleterious and a small fraction are beneficial.
PLG:
I agree. I must also state that variation is not an evolutionary concept at all. It was adopted by evolutionary theorists in an attempt to save their theory, but not even that has helped them except to the non-thinking masses (not directed at you).
M: I encourage you to then actually read Darwin's Origin of Species as the entire theory and most of Darwin's writings were focused on variation. All evolutionary theorists including those pre-dating Darwin were drawing their conclusions based on observed variation within and among species....evolution is the study of variation over time.
PLG: Again, if we define evolution simply as "change", then yes, population genetics is "evolution". But evolution is not simply change (playing word games again), it is about speciation. One organism giving rise to another different kind of organism altogether, and this has never been demonstrated as even a possibility. Every time this is addressed, it is addressed as speculation, and most often in "matter-of-fact" wording when the fact is not codified, nor can be.
M: You are actually both playing with words and demonstrating a fatal misconception about evolution. First, if speciation is not change then what is your definition of change? Fixation of a specific allele in a population is as much a part of change as is speciation. Second, and this is one of the oldest creationist claims I have seen...that one organism has to turn into another...this is exactly what evolution says does NOT happen..at least not Darwinian....that is what Lamark and others proposed. Observed speciation events have been observed both in laboratory settings and in the wild:
Schliewen UK, Tautz D, Paabo S. Related Articles, Links
Sympatric speciation suggested by monophyly of crater lake cichlids.
Nature. 1994 Apr 14;368(6472):629-32.
My earlier post on bacteria also showed evolution over 20,000 generations.
Savolainen R, Vepsalainen K. Related Articles, Links
Sympatric speciation through intraspecific social parasitism.
Proc Natl Acad Sci U S A. 2003 May 9 [epub ahead of print]
in den Bosch HA, Odierna G, Aprea G, Barucca M, Canapa A, Capriglione T, Olmo E.
Karyological and genetic variation in Middle Eastern lacertid lizards, Lacerta laevis and the Lacerta kulzeri complex: a case of chromosomal allopatric speciation.
Chromosome Res. 2003;11(2):165-78.
There are many many more examples.
But evolutionary theory DOES NOT hypothesize that your cat will turn into a dog.
PLG:
What I meant was that the gene pool of a species has boundaries which the species cannot go beyond. This has been known and understood now for nearly 5,000 - 10,000 years of animal husbandry and breeding. As I understood from one of Mayr's books (I can't remember which one right off the top of my head), he acknowledged this fact and then went on to say that mutation originates variation which can push the species over the old gene pool limitations, opening the way for speciation and evolutionary furtherance.
To date, I have not read any articles demonstrating that variation can add novelties to a species gene pool that can take it beyond those limits. Do you know of any?
M: There are thousands of examples...however, you will have to show real evidence of a limit to the gene pool...this is just plain wrong..what is the limit then? How can that limit explain the old C value paradox? There appears to be no limits on variation in the gene pool that I have ever heard of or been aware of...as to novelties..there are thousands of examples but I will list one of my favorites:
Mi S, Lee X, Li X, Veldman GM, Finnerty H, Racie L, LaVallie E, Tang XY, Edouard P, Howes S, Keith JC Jr, McCoy JM. Links
Syncytin is a captive retroviral envelope protein involved in human placental morphogenesis.
Nature. 2000 Feb 17;403(6771):785-9.
This retroviral gene entered the primate gene pool and took over the function of syncitiotrophoblast formation and thus is largely responsible for proper placenta formation.
Other examples are the tranmission of antibiotic resistance genes among bacteria by conjugation....
It is actually rather hard to answer your questions as the premise is incorrect, there are no limits so I am not sure what you actually then mean by novelties beyond those limits..
PLG:
OK, so here we go. The bacteria was still a bacteria, was it not? Then it did not speciate. Same goes for cichlids and all of the plants that have been shown to me thus far. The criteria on which the so-called "speciation" must be examined, and in most cases there are so many special circumstances as to warrant a "recall" in my mind.
And when I say one species turning into another, I mean one species giving rise to another. I know one animal does not turn into another, so please do not insult my intelligence. This is the problem with evolutionary theory in general. Generalities are spoken when the issue is to avoid the specifics, and specifics are spoken when the issue is to avoid the generalites. Darwin did not wirte a thesis on change for change's sake, but in addressing speciation, therefore addressing evolution as speciation, not change. So why do modern evolutionists cling to "change" being evolution, when evolution is supposed to be all about explaining the origin of species? Genetic change does not give credence to evolution without definite, one-sided evidence, which it does not have.
M: On the one hand, you say the bacteria are still bacteria...on the other hand you claim I am insulting your intelligence by claiming you think one organism does not turn into another and also make a completely incomrehensible statement like "And when I say one species turning into another, I mean one species giving rise to another. "
Again, why is speciation not change? Do you expect a cichlid to speciate into a non-fish? That seems to be your definition of evolution. Loxodonta africana and Elephas maximus (African and Asian elephants respectively) are both elephants...they are genetically very similar, there was even one successful birth of a hybrid..well sort of successful..it died after 10 days...both are a different species...different genus in fact...if they were to speciate again they would not turn into cichlids..in fact, it has been discovered that the forest elephant, Loxodonta cyclotis, is genetically very different from the savanah elephants Loxodonta africana. They can interbreed but even when presented the opportunity they do not. Morhologically, the forest elephants are adapted to forest life to a mild degree...they are so genetically distinct that they are now given species level distinction..thus, a population of savanah elephants have adapted to the forest and have become genetically and morphologically distinct...this is how evolution works...not the an elephant species giving rise to a dog.
PLG: Not so. I was saying that Mayr went outside the scientific method, I am saying that he was not doing science, but making up stories to suit his percieved needs in order to keep the theory alive.
M: This is mere assertion..please support it...and while you are at it please show that you know how the scientific method works before you make such foolish assertions.
PLG: I have heard of it, and you are missing one small detail. You cannot claim hox genes unless you are going to give some kind of evidence that they, too, can come about from nothing down the evolutionary pathway. This is typical, "matter-of-fact" statements such as the claw of this certain crab was modified from mouth parts in its ancestors. This is not a scientific explanation of anything, it is, instead, a matter-of-fact statement based upon the opinion of the writer, based upon the unconfirmed assumption that evolution is a fact of nature.
M: This is a complete logical fallacy. First of all, you are muddling up abiogenesis with evolution because you are stating I have to know what the last common ancester Hox gene was to study Hox genes now which is just plain stupid. Second, I can trace the evolution of Hox genes from simple organisms to complex with the observed increase in complexity of the pathway...look up amphioxous for example..it has a relatively primitive Hox cluster and has a simple segmentation routine and compare to more complex organisms Hox clusters..this does not a priori assume evolution as you state. In the comparison the most parsimonious answer is common ancestry i.e. identity by descent i.e. evolution.....one does not a priori assume evolution is true and then bend the data to fit it...that is why you clearly have a warped and incorrect view of science and the scientific method.
PLG:
I will say it again, and then I have to go for now. What needs to be done is the assumption of evolution needs to be dropped from science altogether - every reference to evolutionary theory - and then begin again from scratch. From step one, and then have the process heavily monitored so that it only sticks with the facts. New terminology would undoubtedly be developed, and some old terminology would undoubtedly be dropped.
M: No, you have to drop your childish assumption that the big bad scientific establishment is out to get you personally. What you describe as the scientific method is absolutely ass backwards and actually fits much better with how relgious apologetics works...The theory of evolution was developed as the best explanation for the natural variation of life on the planet. It is supported by evidence from multiple varied disciplines from biology to paleontology...it is a theory because it is one of the best tested falsfiable hypotheses in the history of science..it is constantly being challenged by scientists today and revised accordingly..it has a more solid foundation than the theory of gravity or relativity. Thus, until their is a scientific reason presented in the form of data i.e. the genome sequence of a cichlid is more similar to marsupials than other fish would do a good job of killing off evolution..and genetic for that matter...there is no reason to revise science as you would have it.
I am still waiting for you to describe how the scientific method works..in attempting your definiton could you include definitions for
1: hypothesis
2: theory
3: fact
4: evolution
Throughout your posts to me and to others it is very clear to me that you may be confused about the meanings of each of these. I will be happy to discuss each one with you when you get the time.
As to your lack of time and long pauses between posts, don't worry about it..I think everyone here understands that you cannot post here 24 hours a day. I personally would prefer a longer pause and a solid effort to address my questions and rebuttals than a quick response with less content...thus far you seem to be making an honest effort even though I completey disagree with you on most issues so I commend you for it.
cheers,
M
™ Version 4.2