Potential falsifications of the theory of evolution

We do have evidence that Hox genes duplicated and diverged through evolutionary mechanisms.The problem I have with the constant reference to "Darwinian evolution" is that no one uses the theory put forward by Darwin. It has changed quite a bit in the last 150 years. Shapiro is beating a dead horse. What Shapiro is arguing against is the myopic view that point mutations are the primary driver of evolution. I agree with him. Let's use heliocentrism as an analogy. Let's say that Galileo, the father of heliocentrism, put forward the statement that the Earth moved about the Sun in a circular orbit. Through time we discovered that the Earth does not follow a circular orbit, it follows an elliptical orbit. Have we just falsified heliocentrism? Perhaps we have falsified Galilean heliocentrism, but have we falsified heliocentrism itself?Let's go even further. Galilean heliocentrism also incorporated gravity at some point and proferred the mechanism that the Sun pulled on the Earth which resulted in the observed orbit. Later on it was found that the gravitational pull of Jupiter also influenced Earth's orbit. Have we falsified heliocentrism once again because the original formulation did not include Jupiter's influence on the orbit of Earth?Now that we have falsified Galilean heliocentrism on two points can we now suggest that the Sun actually orbits the Earth? Can we now argue that it is invisible fairies pushing the planets around in the night sky?

You have made a lot of claims over the past few posts so I will only address a few:Please show how Behe has distorted or treated anything Shapiro has said unfairly? What does this even mean? What is an evolutionary process? No one is arguing that things aren't changing (evolving) the question is how. To simply call the "how" an evolutionary process makes no sense.I have read his papers. I have also read his response to Dembski's question about how these non-random systems could have arisen in the first place, and I have read Shapiro's reply: "Where they come from in the first place is not a question we can realistically answer now, any more than we can explain the origin of the first cells."In light of this, Shapiro really doesn't have much to offer about the "naturalism" of such mechanisms, now does he?Furthermore he has said: As such I don't need someone else, or even Shapiro to interpret that for me.In fact, if anyone, including Behe says that this information supports ID, even if Shapiro himself says it doesn't support ID, based on the fact that Shapiro has already stated that he has no idea where these systems arose, any further opinion Shapiro has on the roots of intelligence of these systems is meaningless. Shapiro has no idea how they arose, so how can he say it doesn't support ID?AND, the most pertinent point, is that this is what ID proponents have been suggesting and predicting all along! Long before this information ever came to light, people like me and many others have been telling you until we are blue that your one mutation, then wait awhile, then another mutation then wait awhile scenario is a load of crap. In fact I have hypothesized about this extensively not only here but other places for years, that there is SOME mechanism, as yet not fully known, that does exactly what Shapiro is now calling natural genetic engineering. That cells don't wait for a fortuitous mutation, but rather they create their own adaptive success. Prediction, research, confirm prediction. That is science. Gee imagine that, dumb creationists can't even read a biology book, and yet somehow it is turning out exactly like we predicted.So do I feel like I have the right to claim the intellectual high-ground now? The answer is, hell yes. And it is only going to continue to get more and more obvious. "Lucky mutation, wait awhile, another lucky mutation, wait a while more, and a million years later, something might happen" Yea Bullshit. Go read another biology book, and get one for Dr. A.

The fact that Behe asserts that Shapiro's findings suggest Intelligent Design when Shapiro's findings suggest nothing of the like. A process whereby heritable variation is created that is independent of fitness, and then this variation is passed through selection. Again, you are confusing origin with action. The activity of these mechanisms is completely natural. No outside supernatural entities are required for DNA regulators to bind to DNA. The mutations that these processes produce are still random with respect to fitness, in line with neo-Darwinism.Also, Shapiro states quite clearly that we don't know NOW how these systems came to be. In classic ID fashion, this is mistranslated into "we can never know, therefore magical poofing". Obviously, you do given your next statement: How does "I don't know" equate to "God . . . err, the Intelligent Designer did it"? You are putting your own biases into Shapiro's statements. That is not what Shapiro is saying. What Shapiro is saying is that cells increase their random mutation and DNA recombination rates when they encounter environmental stress. These changes are still random with respect to fitness. The intelligence of these systems is within the systems, not from an ouside source. According to Shapiro, it is "lucky DNA recombination event, wait awhile, lucky DNA recombination event, wait awhile, and a million years later something has happened". Are you willing to accept that?

How can you demonstrate that Shapiro's findings don't suggest intelligent design. Because of Shapiro's opinion? That's just his opinion, why should that be the final word. One thing we do know for sure is that he doesn't feel Darwinism is sufficient to explain it, so what is left?And do you even have any wordings from Behe to have a contention with anyhow?What many evolutionists fail to want to grasp is that without Darwinian evolution, you have nowhere to go other than a direction. With Darwinian concepts you could argue for completely unguided randomness, and this is what has given people like Dawkins and Granny such solace (and oh how they have loved this comfort). As long as you had that, you could claim it is all just lucky chaos. Some of course won't want to let that lucky chaos go (deny deny deny, a tried and true defense) so they will try to drag Darwin as far down the road as they can. But there isn't much left there to drag. Ha, no I would say you are the one confusing natural with unguided. What Shapiro is describing is decidedly not random. If you don't think so, you better go read him so more. He is describing purposeful mechanisms. The obvious question that needs to be answered is WHERE DID THEY GET THEIR PURPOSE?You can't just sweep that under the rug and expect to have any credibility about any claims for a random world.No these are not random mutations. But if you want to try natural selection without your needed randomness--good luck. Nope, you better do some more reading. He is saying that is nothing lucky about it at all. The cell is smart so it doesn't need luck. Sorry to interrupt your worldview.On your final point about IDsts wanting to create a God where knowledge doesn't exist I just don't buy that argument. You have a choice of two: randomness or guidance (unless you can somehow come up with a third choice).As the needle swings back and forth between our two options, the further it strays from randomness the closer it edges towards guidance. That's just the nature of the two choice world. Edited by Bolder-dash, : No reason given.

What is it about Shapiro's findings that you think suggests intelligent design? Shapiro certainly doesn't think they do. Even minute examination of life's processes reveals nothing more than natural processes. Where in these processes do you see evidence for an intelligent designer? In their complexity? That's just the old tired claim of intelligent design, that life is too complex to have risen and evolved naturally. None of the evidence that would be apparent if an intelligent designer were at work, such as non-nested relationships between at least some species, or novelty arising in a single generation, has ever been observed. Shapiro certainly offers no help for intelligent design.Creationists are latching onto Shapiro because he expresses himself in ways that they interpret as supportive of intelligent design. The reality is that Shapiro doesn't support intelligent design, and that's because his research doesn't support intelligent design. What his research does suggest to him is that the mechanisms of evolution are so far beyond what was originally conceived in the 1920's when the modern synthesis between Darwinian evolution and genetics arose that he has come to believe that it should be replaced with a more varied and nuanced framework. Most others disagree, pointing out that the 80 year old framework *has* changed a great deal and has already incorporated the ideas he enumerates. Mutation is random, selection is not. Evolution includes both mutation and selection and cannot be described as "completely unguided randomness." In Message 624 you listed a bunch of processes that you labeled "adaptive intelligent responses" (I've edited this to make it more readable): If the effect of any of these on the genome is non-random then you should be able to tell us what that effect will be. Pick one or two and tell us the specific changes they will cause to the genes of individuals. You won't be able to do this because when Shapiro says non-random he doesn't mean guided and certainly not deterministic. You've already made a few wrong choices. Your first wrong choice was in deciding to continually mischaracterize evolution as random. Mutations are random, selection is not.Your second wrong choice is in thinking of the issue as either/or. It's not. The issue is following the evidence where it leads. When we examine life all we see is matter and energy following known laws of chemistry and physics.Your third wrong choice is equating complexity with design. Cars and computers are examples of complexity designed by people. Kangaroos and kumquats are examples of complexity designed by nature.--Percy

Because none of them involve a supernatural mechanism or outside intelligence. A new theory of evolution. So where did we go when Darwin's own suggestions on the mechanisms of heredity turned out to be false after the discovery of Mendelian genetics? We moved to a new theory of evolution, the Modern Synthesis. Where are we going with all of these new findings? Towards a new theory of evolution.You seem to think that the theory of evolution is set in concrete or something. It isn't. It is ever changing as it incorporates new information. However, nothing we have found thus far has put the major tenets in doubt, those being that mutations are random with respect to fitness and that these mutations are affected by natural selection to one degree or another. We observe lucky chaos that is then filtered through natural selection. When transposon activity is induced by environmental stress, as discussed by Shapiro, it is complete chaos within the genome. They insert all over the place. Some of these insertions are neutral, some are beneficial, and some are detrimental as with all mutations. Random with repsect to what? Unguided with respect to what?Does natural selection guide a population towards higher fitness? Yes. Is natural selection intelligent? No. Do gene regulators guide protein expression? Yes. Are gene regulators intelligent? No. Is gene regulation a smart way to do things from a backwards looking teleological position? Yes. Does this imply that an intelligence constructed the system? No.Can I say that the lottery is not random because the numbers are always between 1 and 50 instead of any number as a truly random process should be? Is the roll of the dice in Craps non-random because 7 is a more common result than 12? Both of these processes are random WITH RESPECT TO THE BET. Mutations are the same. They are random with respect to fitness. Mutations are not random with respect to time and genomic space, but they are random with respect to fitness. When you say that something is non-random you need to supply the context, otherwise it is meaningless. They got that purpose from the process of evolution, the same process that gives purpose to evolved antibiotic resistance in bacteria and evolved beta-galactosidase enzymes and nylonase enzymes. So how do you explain mutations that cause disease? Do parents purposefully give their children hemophilia by specifically and purposefully choosing the mutations that will give them hemophilia? Do parents purposefully create chromosomal rearrangements so that their children will have Turner or Down's Syndrome? Do cells purposefully become cancerous by changing their DNA arrangements and methylation patterns? Then please cite an example where DNA is mutated in a specific manner every time it is challenged with a specific challenge that always results in a beneficial change that is the inherited by the next generation. Shapiro doesn't cite a single example of this. You say you don't buy the argument and then you prove my point in the very next sentence. Nice job.

perch writes, Thank you for your honestyShapiro in The Boston Review in 2006 wrote; Since my interpretations are invalid, how would you interpert this quotation from Shapiro?I interpret it to mean random mutation and selection cannot account for all the modularity, complexity, and integration that arose and changed during the history of life..Edited by shadow71, : No reason given.

I interpret this as the theory of evolution needing to incorporate the idea that selection acts on the interaction of many genes, not a single gene in isolation. Also, mutations that change the interactions between these genes, be it in changing genomic position or a change in a gene regulator, plays a large role in selectable variation. When a gene is turned on and to what extenct is as important as the actual protein sequence of the gene itself. The problem I see with this interpretation is that you are taking specific types of selection and mutation that Shapiro talks about and apply it to all selection and all mutations. This is a big mistake, IMHO.Edited by Taq, : No reason given.Edited by Taq, : No reason given.

Shapiro merely substitutes "modular units" into the mutation + natural selection = evolution formula.01/07/30 - ICBP 2000 Note! It's the biochemical pathways that move the modules that are nonrandom. Not the mutation. Edited by molbiogirl, : No reason given.

Just between you and me, a lot of what Shapiro goes on and on about sounds an awful lot like "OMG!!! Epigenetics!!11!!"

Thanks Taq for your very information. I have a question for you.Taq wrote; Shapiro wrote in the Boston Review 2006;"How all of this modularity, complexity, and integration arose and changed during the history of life on earth is a central evolutionary question. Localized random mutation, selection operating 'one gene at a time' (John Maynard Smith's formulation),and gradual modification of individual functions are unable to provide satisfactory explanation for the molecular data, no matter how much time for change is assumed. There are too many potential degrees of freedom for random variability and too many interconnections to account for."Does this quote agree with what you posted above?

That's my take on it too. Sometimes he sounds like a high schooler who comes home with a proud look on his face while he tells everyone how light can be both a wave and a particle as if it was earth shattering news. I don't want to say that Shapiro's article is much ado about nothing because it is important, but it is hardly new. He never seems to get beyond his own descriptions of these systems to the more important questions within the theory of evolution. Of course, this is only a review article so generalizations are expected.For example, he makes a big deal of the tendency for transposons to insert up stream of genes and act as gene regulators. Well, that is great and all but what does this mean with respect to evolution and fitness? What if this results in the gene being turned on when it should be off, or overexpressed? What if this gene is involved in the cell cycle? What if the disregulation of this gene results in unrestrained replication along with a lack of cell contact inhibition? I believe they call that cancer.Shapiro is a good salesman, I will give him that.Edited by Taq, : No reason given.

It is tangential to the issue of the randomness of mutations. What Shapiro is talking about is the old paradigm of one-gene, one-feature. This is where variation is primarily driven by point mutations in genes, and each mutation is modular or singular in it's actions. Biology has left this paradigm in it's rear view mirror well before Shapiro published the article in question. Biology has switftly adopted the Evo-Devo view of evolution where gene regulation plays a very important role in evolution. With the DNA revolution it was finally possible to link embryonic development (Devo) with the evolution of DNA sequence (Evo), and with it came the understanding that gene regulation plays a very important role in overall fitness.To put this in plainer terms, Shapiro is beating a dead horse and trying to look fancy while he is doing it.

molbiogirl writes; First of all I said in the post " Shapiro writes," and then placed findings that I relied on in the post as you asked me to do. .plagiarism is defined as: the practice of taking someone else's work or ideas and passing them on as one's own.So I accept your apology for calling me a plagiarist.molbiogirl further wrote; You seem to think that random mutation and natural slection as per the modern theory are synonymous with Shapiro's "Natural Genetic Engineering", that is not so.
Shapiro explicit states in many writings including this quote from the Boston Review paper;"The possibility of a non-Darwinian scientific theory of evolution is virtually never considered. In my comments, then, I propose to sketch some developments in contemporary life science that suggest shortcomings in orthodox evolutionary theory and open the door to very different ways of formulating questions about the evolutionary process. After a discussion of technical advances in our views about genome organization and the mechanisms of genetic change, I will focus on a growing convergence between biology and information science which offers the potential for scientific investigation of possible intelligent cellular action in evolution."That I suggest, again, is evidence that Shapiro does not fully agree with the modern theory of evolution of random mutation and natural selection.
In the least he is discussing a built in information system in the cell.Edited by shadow71, : correct typo's

Come now, shadow.
You promised.And what say you to writing Shapiro?
Seems a pretty simple way to settle the question, does it not?
And he seems amenable to e mail correspondence with IDists. http://www.iscid.org/james-shapiro-postchat.php