Miller’s meanderings: only the same bogus contentions

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Genetic fallacy. The points I made stand independent of your personal feelings towards me.

That's not the meaning of the term evolution utilized here, that's natural selection which is a component of evolution. Instead what is meant is the General Theory of Evolution.

Consider,

Firstly, educated scientists can sometimes know that induction and causality are not entirely valid, but rather they can take the whole matter in a Popperian or semi-Popperian manner, which is to say that we theorize and these theories predict and/or fail to be disconfirmed by the evidence. I say "semi-Popperian" because reasonable scientists and philosophers/historians of science recognize that no great theory gets thrown out because of a problem in one observation, particularly given that this one observation could possibly be explained away later in many circumstances.

The rule about direct observation really doesn't matter so much given that scientific explanations of reality are often still considered science, just not laboratory science. Such a rule that all science must be laboratory science would outright exclude a lot of social scientific inquiry, as well as cosmology, geology, etc. The problem is that such a rigidity of definition just makes no sense, as the logical method of inquiry bears some similarity to actual science, and the knowledge used has overlaps with laboratory science. I wouldn't necessarily call this the same as "origins science" although I can see how a creationist might, but given that economics, sociology, and anthropology cannot have a laboratory component, but are not origins, I think the labeling scheme is obviously flawed.

Now, I would probably disagree somewhat with Lewonton's skepticism (and I wouldn't even know his context, as anybody could say anything in any context to make any point.)

Even further, I would also tend to agree with the naive view "follows the evidence wherever it leads", but that's because I think my view is correct, and also because I think that despite the flaws and problems, generally science does this and to some extent, I'd bet the biases likely make science better than the robots. The fact that creationists are open about their bias does not make them more honest though.

David Hull's statement doesn't really help Sarfati's point as far as I can see.

Todd's statement also doesn't prove anything, because we also know that most of the data points away from an intelligent designer. He's just being consistent to a set of philosophical presuppositions. Even then though, what he says wouldn't matter because scientists are philosophically naive and no one scientist determines the path of all science.

I don't see the use of examples of evolution in progress to be a bait-and-switch either, or even improper. I mean, no, these don't literally prove evolution, but they certainly show that evolution is a really great explanation, and possibly can be used to show that it is the best explanation that we have.

Firstly, educated scientists can sometimes know that induction and causality are not entirely valid, but rather they can take the whole matter in a Popperian or semi-Popperian manner, which is to say that we theorize and these theories predict and/or fail to be disconfirmed by the evidence. I say "semi-Popperian" because reasonable scientists and philosophers/historians of science recognize that no great theory gets thrown out because of a problem in one observation, particularly given that this one observation could possibly be explained away later in many circumstances.

The rule about direct observation really doesn't matter so much given that scientific explanations of reality are often still considered science, just not laboratory science. Such a rule that all science must be laboratory science would outright exclude a lot of social scientific inquiry, as well as cosmology, geology, etc. The problem is that such a rigidity of definition just makes no sense, as the logical method of inquiry bears some similarity to actual science, and the knowledge used has overlaps with laboratory science. I wouldn't necessarily call this the same as "origins science" although I can see how a creationist might, but given that economics, sociology, and anthropology cannot have a laboratory component, but are not origins, I think the labeling scheme is obviously flawed.

Now, I would probably disagree somewhat with Lewonton's skepticism (and I wouldn't even know his context, as anybody could say anything in any context to make any point.)

Even further, I would also tend to agree with the naive view "follows the evidence wherever it leads", but that's because I think my view is correct, and also because I think that despite the flaws and problems, generally science does this and to some extent, I'd bet the biases likely make science better than the robots. The fact that creationists are open about their bias does not make them more honest though.

David Hull's statement doesn't really help Sarfati's point as far as I can see.

Todd's statement also doesn't prove anything, because we also know that most of the data points away from an intelligent designer. He's just being consistent to a set of philosophical presuppositions. Even then though, what he says wouldn't matter because scientists are philosophically naive and no one scientist determines the path of all science.

I don't see the use of examples of evolution in progress to be a bait-and-switch either, or even improper. I mean, no, these don't literally prove evolution, but they certainly show that evolution is a really great explanation, and possibly can be used to show that it is the best explanation that we have.

Evolution has been proven beyond any doubt to be occuring. There have been hundreds if not thousands of studies showing it in action. eg. warfarin resistance in rat's,viral evolution, antibiotic resistance in bacteria.

i think that you should really be willing to accept criticism if you are posting a quote of a criticism of someones work. (millers) it seems a tad hypocrytical.

also i would like a reply to my first post. please tell me why (if you do?) you do not believe a myriad of observational studies to show evolution in action.

I suppose so. Induction is inherently flawed, especially when dealing with human or animal behavior, but when dealing with more purely physical phenomena such as projectile motion, electric current, spectra, etcetera, the induction is able to be a lot more valid since the results are usually demonstrably repeatable. Popper had, as far as I can see, realized that the deductive process of denying the consequent had more validity than induction which can be likened to the fallacy of affirming the consequent. However, the inductive process, at least in regard to physics and chemistry, has led to the technological development of electronics and complex mechanical apparatus such as aircraft and automobiles in general.

Laboratory sciences are usually stronger in validity than social sciences though. A statistical generalization of one era or within one culture may or may not be generally true within another era or another culture. In economics, I consider items such as "elasticity of demand" to be somewhat ad hoc in that the various terms of perfect elasticity, perfect inelasticity, etc along with their mathematical definitions to be a form of labeling as to why supply doesn't affect the demand of different types of items in the same manner. Such nomenclature and labeling is useful in a market, though, to see how consumers in a market alter the quantity they demand of various items based on their supply or price for a given period of time, but even still such types of demand of items may alter as the constituent members of the market die off and are replaced by yet another generation.

Well, here is part of the context, although the full context requires membership with the New York Book review so I couldn't read it all, but here is the link, http://www.nybooks.com/articles/archive ... of-demons/

I think that although it may not make one more honest to admit to their bias openly, it does help with individual intellectual honesty to realize that everyone including one's own person has bias, or as Dr Sarfati said in a response to one of his facebook statuses, "Everyone with an IQ above freezing point has a bias..."

The making of observations alone would imply that the facts speak for themselves. However, in the process of making inferences from the observed data the inferences themselves will be colored by the bias of the observer. If the observer recognizes their bias, then they have more ability to recognize that they have a tendency to make only inferences which automatically confirm their bias and thereby more ability to counter their own biases. But scientists and laymen who don't recognize their own bias but assume their own objectivity thereby blind themselves.

No, but organizations such as a nation's National Academy Of Sciences and other organizations of the like set the tone for the majority to follow. To an extent, there may be a bandwagon mentality that plays a role, I think.

The thing is that people don't agree on terms and often use them interchangeably, perhaps unintentionally, but still incorrectly when in the context of an argument. Sometimes people call "natural selection" by the name of "evolution", and then show examples of natural selection in action since that is actually observable, and then they claim that evolution is true because natural selection is true. E.g.

They show natural selection in action, not evolution. The evolution required to build microbes into mankind requires not just natural selection alone, but also variation. It needs to be shown that the kind of variation required occurs, a kind of variation which produces novel genes for novel organs. Proving natural selection does not prove that this type of variation occurs because natural selection acts upon pre-existent genes alone.

That variation exists (and is constantly produced by meiosis and a variety of different sources of mutation) is quite well established.

And there have been a few studies where genetic adaptation appeared to actually follow phenotypic changes, rather than the other way around as is usually expected. I will have to check the technical details again, but it is important always to keep in mind that biology is a lot more complicated than we think.

That variation exists (and is constantly produced by meiosis and a variety of different sources of mutation) is quite well established.

And there have been a few studies where genetic adaptation appeared to actually follow phenotypic changes, rather than the other way around as is usually expected. I will have to check the technical details again, but it is important always to keep in mind that biology is a lot more complicated than we think.

I'm not arguing against the existence of variation. Rather the type of variation which is required to produce new organs, or at least new organelles, needs to be demonstrated empirically in the present repeatably prior to the pond-scum to invertebrates to fish to lung-fish to amphibians to yadda-yadda form of evolution being accepted as remotely possible.

Hm. There have been a number of papers on evolutionary novelty, and we have observed the development of novel traits (such as entire metabolic pathways). Observing new organs is less likely to happen in the near future as most genomics research is done on microbes. New organelles—I'll have to check around on that, but off the top of my head I don't think there's been as much research in organelle evolution yet.

Multiple Mutations Needed for E. Coli

3:35 PM PDT, June 6, 2008
Dear Readers,

An interesting paper has just appeared in the Proceedings of the National Academy of Sciences, “Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli.” (1) It is the “inaugural article” of Richard Lenski, who was recently elected to the National Academy. Lenski, of course, is well known for conducting the longest, most detailed “lab evolution” experiment in history, growing the bacterium E. coli continuously for about twenty years in his Michigan State lab. For the fast-growing bug, that’s over 40,000 generations!

I discuss Lenski’s fascinating work in Chapter 7 of The Edge of Evolution, pointing out that all of the beneficial mutations identified from the studies so far seem to have been degradative ones, where functioning genes are knocked out or rendered less active. So random mutation much more easily breaks genes than builds them, even when it helps an organism to survive. That’s a very important point. A process which breaks genes so easily is not one that is going to build up complex coherent molecular systems of many proteins, which fill the cell.

In his new paper Lenski reports that, after 30,000 generations, one of his lines of cells has developed the ability to utilize citrate as a food source in the presence of oxygen. (E. coli in the wild can’t do that.) Now, wild E. coli already has a number of enzymes that normally use citrate and can digest it (it’s not some exotic chemical the bacterium has never seen before). However, the wild bacterium lacks an enzyme called a “citrate permease” which can transport citrate from outside the cell through the cell’s membrane into its interior. So all the bacterium needed to do to use citrate was to find a way to get it into the cell. The rest of the machinery for its metabolism was already there. As Lenski put it, “The only known barrier to aerobic growth on citrate is its inability to transport citrate under oxic conditions.” (1)

Other workers (cited by Lenski) in the past several decades have also identified mutant E. coli that could use citrate as a food source. In one instance the mutation wasn’t tracked down. (2) In another instance a protein coded by a gene called citT, which normally transports citrate in the absence of oxygen, was overexpressed. (3) The overexpressed protein allowed E. coli to grow on citrate in the presence of oxygen. It seems likely that Lenski’s mutant will turn out to be either this gene or another of the bacterium’s citrate-using genes, tweaked a bit to allow it to transport citrate in the presence of oxygen. (He hasn’t yet tracked down the mutation.)

The major point Lenski emphasizes in the paper is the historical contingency of the new ability. It took trillions of cells and 30,000 generations to develop it, and only one of a dozen lines of cells did so. What’s more, Lenski carefully went back to cells from the same line he had frozen away after evolving for fewer generations and showed that, for the most part, only cells that had evolved at least 20,000 generations could give rise to the citrate-using mutation. From this he deduced that a previous, lucky mutation had arisen in the one line, a mutation which was needed before a second mutation could give rise to the new ability. The other lines of cells hadn’t acquired the first, necessary, lucky, “potentiating” (1) mutation, so they couldn’t go on to develop the second mutation that allows citrate use. Lenski argues this supports the view of the late Steven Jay Gould that evolution is quirky and full of contingency. Chance mutations can push the path of evolution one way or another, and if the “tape of life” on earth were re-wound, it’s very likely evolution would take a completely different path than it has.

I think the results fit a lot more easily into the viewpoint of The Edge of Evolution. One of the major points of the book was that if only one mutation is needed to confer some ability, then Darwinian evolution has little problem finding it. But if more than one is needed, the probability of getting all the right ones grows exponentially worse. “If two mutations have to occur before there is a net beneficial effect — if an intermediate state is harmful, or less fit than the starting state — then there is already a big evolutionary problem.” (4) And what if more than two are needed? The task quickly gets out of reach of random mutation.

To get a feel for the clumsy ineffectiveness of random mutation and selection, consider that the workers in Lenski’s lab had routinely been growing E. coli all these years in a soup that contained a small amount of the sugar glucose (which they digest easily), plus about ten times as much citrate. Like so many cellular versions of Tantalus, for tens of thousands of generations trillions of cells were bathed in a solution with an abundance of food — citrate — that was just beyond their reach, outside the cell. Instead of using the unreachable food, however, the cells were condemned to starve after metabolizing the tiny bit of glucose in the medium — until an improbable series of mutations apparently occurred. As Lenski and co-workers observe: (1)

Such a low rate suggests that the final mutation to Cit+ is not a point mutation but instead involves some rarer class of mutation or perhaps multiple mutations. The possibility of multiple mutations is especially relevant, given our evidence that the emergence of Cit+ colonies on MC plates involved events both during the growth of cultures before plating and during prolonged incubation on the plates.

In The Edge of Evolution I had argued that the extreme rarity of the development of chloroquine resistance in malaria was likely the result of the need for several mutations to occur before the trait appeared. Even though the evolutionary literature contains discussions of multiple mutations (5), Darwinian reviewers drew back in horror, acted as if I had blasphemed, and argued desperately that a series of single beneficial mutations certainly could do the trick. Now here we have Richard Lenski affirming that the evolution of some pretty simple cellular features likely requires multiple mutations.

If the development of many of the features of the cell required multiple mutations during the course of evolution, then the cell is beyond Darwinian explanation. I show in The Edge of Evolution that it is very reasonable to conclude they did.

References

1. Blount, Z.D., Borland, C.Z., and Lenski, R.E. 2008. Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. Proc. Natl. Acad. Sci. U. S. A 105:7899-7906.

2. Hall, B.G. 1982. Chromosomal mutation for citrate utilization by Escherichia coli K-12. J. Bacteriol. 151:269-273.

3. Pos, K.M., Dimroth, P., and Bott, M. 1998. The Escherichia coli citrate carrier CitT: a member of a novel eubacterial transporter family related to the 2-oxoglutarate/malate translocator from spinach chloroplasts. J. Bacteriol. 180:4160-4165.

4. Behe, M.J. 2007. The Edge of Evolution: the search for the limits of Darwinism. Free Press: New York, p. 106.

5. Orr, H.A. 2003. A minimum on the mean number of steps taken in adaptive walks. J. Theor. Biol. 220:241-247.

I discuss Lenski’s fascinating work in Chapter 7 of The Edge of Evolution, pointing out that all of the beneficial mutations identified from the studies so far seem to have been degradative ones, where functioning genes are knocked out or rendered less active. So random mutation much more easily breaks genes than builds them, even when it helps an organism to survive. That’s a very important point. A process which breaks genes so easily is not one that is going to build up complex coherent molecular systems of many proteins, which fill the cell.

who wrote this?

Who wrote this? What?! In the second sentence of the two solitary sentences I wrote I gave the author's name. In the text you quoted the first sentence starts with, "I discuss Lenski’s fascinating work in Chapter 7 of The Edge of Evolution,..." and I gave a link at the bottom of my reply.

ok. i was not really paying that much attention except to the part in bold. what do you have to say in response? i'm sorry but if any one single sentence like that can be so wrong then i need not read the rest.