Potential falsifications of the theory of evolution

Percy writes; I think this might be a good time to clear up your "Creationist" references. Would you please define what you mean by a Creationist?If it means that I believe that God, in his way, created the Universe, including the earth and all organisms of the earth, then I am a Creationist.If you mean by Creationist that the earth was created 10,000 years ago then I am not a Creationist.You continually challenge me for not being precise, I was also ask that you be precise and tell what you mean by Creationist.

Percy writes; Just so I am clear do you accept his position that there are non-random mutations that are part of the process of variation?If so, even if now it isn't proven that the changes in re fitness are not non-randon , wasn't I correct when I posted that Shapiro's Natural Genetic Engineering is a partial falsification of the modern synthesis or evolution with genetics?

Tell you what, I'll make you a deal. I'll tell you what the creationist label means to me if you begin responding to the detailed explanations being offered in the messages to you instead of responding with yet more Shapiro quotes that give no indication whether you understood the explanations or not, thereby causing people to have to repeat them over and over again. Deal?--Percy

No because as many people have explained modern evolutionary theory does not hinge on mutations being random in the sense of equiprobable, indeed Darwinian evolution in general has never presupposed this. It has been known for decades that the probabilities of certain types of mutation are more likely and that certain regions of the genome or specific genetic sequences are more susceptible to mutation.It is only a falsification of your own strawman conception of what evolutionary theory is.TTFN,WK

The link to Shapiro's talk is James A. Shapiro - Revisiting evolution in the 21st Century. The exact quote from the introductory comments is: There's no mention of intelligent design in the intro. Whoever described Shapiro's approach this way may actually believe that it represents something midway between evolution and creationism. They're welcome to their opinion, and if you want to argue that point of view then go ahead.Later in the presentation at around 21:00 Shapiro ends a point by briefly touching on intelligent design: Later on at around 26:00 Shapiro makes this observation about the complexity of cellular processes: This directly touches on a popular claim of ID, that life appears designed just like many objects we create ourselves appear designed. But even just a single cell is far more complex than anything any team of human beings have ever designed, and that includes the Manhattan project and the Apollo moon program. In complexity but even more in the sheer unexpectedness of the approaches taken, life is unlike anything ever designed by people.Around minute 37 or 38 Shapiro begins describing how bacterial resistance in the real world does not occur in the same way that had been demonstrated in the lab. Laboratory demonstrations of bacterial resistance shows bacteria acquiring mutations through genetic accidents, and by chance some mutations conferred resistance. In the real world Shapiro says that the bacteria become resistant by acquiring new DNA from outside.To Shapiro this apparently comes as so major a departure from the modern synthesis that it must be discarded. Earlier he quotes Francis Crick saying that any deviation from his "central dogma" of vertical-only descent would overturn the theory of evolution, ironically doing the same thing you've been doing of extracting a quote and misinterpreting it. Meanwhile, most of the rest of biology considers horizontal gene transfer as merely yet another way to acquire mutations. The modern synthesis combines Darwinian evolution and genetics, and guess what? Horizontal gene transfer is part of genetics, at least according to vast preponderance of biologists.AbE: (I just found Crick quoted about his central dogma statement over at Wikipedia that makes clear how he really viewed his idea. He apparently was unaware of the unfavorable reception use of the word "dogma" would receive: "I did apprehend this in a vague sort of way but since I thought that all religious beliefs were without foundation, I used the word the way I myself thought about it, not as most of the world does, and simply applied it to a grand hypothesis that, however plausible, had little direct experimental support."(In other words, Crick was describing his own personal hypothesis, not a central dogma that was ever held within biology. As I note later, even Shapiro is aware that processes violating this "central dogma" were known before Crick even graduated from middle school.)But at heart we're talking about a label. If Shapiro wants to discard the modern synthesis, fine, but whatever he replaces it with will still have to include vertical inheritance as by far the largest contributor to descent. In the end he'll have to include all the things he talks on and on about as invalidating the modern synthesis but that most biologists think the modern synthesis already includes, and in the end all you'll have is a name change.One very good point that Shapiro makes is that the cellular control process is not just a matter of DNA => RNA => proteins => action. Molecules react with all other molecules, and DNA is just a very complex molecule. It is not invulnerable to the effects of neighboring molecules, and the simple view advocated by Crick is clearly wrong, but we knew that long, long before Shapiro ever came along. Shapiro even notes that one form of horizontal gene transfer was identified way back in 1928, before the structure of DNA was even identified (it was known that DNA was a vehicle for heredity prior to the discovery of its structure).--PercyEdited by Percy, : Add AbE section.

How are you defining non-random? For you, is a non-random mutation one that is a result of cellular machinery rather than chemical accident, but still one whose nature and effect is highly non-deterministic and therefore unpredictable? If so then you are using non-random in the same sense as Shapiro, and I of course agree that genetic change can be driven by the cell's own internal processes, because that's precisely what the evidence indicates. Shapiro thinks that things like HGT (Horizontal Gene Transfer) invalidate the modern synthesis because HGT wasn't known to geneticists when the modern synthesis was first created. Most of the rest of biology thinks that HGT is already part of the modern synthesis.Shapiro once said that if the modern synthesis can't be invalidated then it is the first invulnerable theory in the history of science, implicitly chastising biologists for clinging to an obsolete theory. But Shapiro is mischaracterizing theory. Theories, like life, are growing and changing all the time. If theories were invalidated every time we discovered something new we would have long ago run out of names for all the new theories. What really happens in science is that new knowledge is incorporated into existing theory.It is exceedingly rare for new knowledge to contradict existing theory so violently that the theory must be discarded, but it *has* happened. I believe there is only one good example, and that was the geological theory of fixed continents. In retrospect overturning this theory wasn't anything too earth-shattering () since it was based on insufficient data, but at the time Wegener first proposed the idea of continental drift it seemed like heresy and blasphemy.--PercyEdited by Percy, : Typo.

I think this is a big part of the problem, 'The modern synthesis' can be interpreted in a number of ways. The orginal 'Modern synthesis' predates virtually all molecular biology, including the elucidation of the structure of DNA by Watson and Crick. It is hardly surprising therefore that this original form, principally built in the late 30s and early 40s, does not take into account things like horizontal gene transfer, discovered in the 50s, or transposable elements, only just being discovered at the end of the 40s.I'd say most biologists nowadays use 'The modern synthesis' or 'neo-darwinian theory' to refer to the ongoing incorporation of the findings of modern genetics, developmental, ecological and other biological disciplines into our understanding of evolution. In this way 'The modern synthesis' can be seen as a moving point representing our best current understanding of how evolution works.It is unfortunate that from time to time some researchers seem to decide that to make their own research seem more revolutionary they have to try to show it overturning some long held dogma or paradigm, and it seems that 'The modern synthesis' or 'neo-darwinian theory' are popular candidates.TTFN,WK

Non-random with respect to what?All Shapiro showed is that mutations are non-random with respect to time and genomic features. He never demonstrated that mutations are non-random with respect to fitness.

Shapiro is wrong. Bacterial resistance occurs through both routes. Scientists do use the word "dogma" in a way that is perhaps misleading. When you ask a scientist what the "current dogma" is with relation to a specific field what you are asking for is the current consensus or theory. A "scientific dogma", if you will, is what a scientist considers to be the safest and most common explanation for a given phenomenon. I think it could easily be argued that "dogma" is not the right word to use, but it is used in this context nonetheless. "Dogma" in no way indicates a strident or immovable opinion when it relates to science. Another idea that Shapiro is right to criticize is the idea of an informational hierarchy within the cell. Wrongly or rightly, students in high school are given the impression that DNA is the almightly boss in the cell. This couldn't be further from the truth. There is really no single pool of molecules that runs the cells. If anything, I would argue that RNA has the strongest influence on the cell, but that is an argument for another day. It is the interaction of all the molecules with their environment that results in the life we see. I think this is what Shapiro is stressing.

What I read from this is that TE mutagenesis creates a lot of variation, some of which is neutral, beneficial, and beneficial. Natural selection then purifies the beneficial TE mutants. This is exactly what the Modern Synthesis predicts, random TE mutagenesis followed by selection.Shapiro agrees with us.

taq writes; My question is has it been demonstrated by experments that all mutations are random with respect to fitness? If so would you please cite me to paper so I can read and understand the proces or logic behind the statement that all mutations are random with respect to fitness.

percy writes; I am defining non-random as deterministic in re a TE that lodges in a loci in a gene in distress to repair that cite. that is what I believe molecuar studies have shown.
You state that all mutations are random in re fitness, as I asked Taq in my last reply, are their actual studies that confirm that, and if so please give me a cite to a paper.

That doesn't even make any sense that I can see. Fitness is determined after the fact. It is totally unrelated to the mutation side.

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Anyone so limited that they can only spell a word one way is severely handicapped!

percyy writes; I take it that you believe that the complexity of such a single cell came about by random accident?Would you agree that it also may have come about by a directed plan?If not, what is the basis of that opinion?

Wounded King writes; So it is your position that mutations may be non-random correct?
May mutations also be non-random with regards to fitness in that
there are probabilities that certain types of mutatons are more likely than not to effect fitness changes?