Potential falsifications of the theory of evolution

Until you understand what random means, you are going to continue to struggle with grasping the new evolutionary discoveries.Shapiro doesn't call these natural genetic engineering systems random (because they are not) I have explained to you exactly how a stress input is directly related to a specific adaptive response (so that's not random), the only thing random here is your definition of the word random. Somehow you think it is connected to a species fitness level-bizarre.In other words, these actives aren't happening just because they just so happened to occur at the same time that the stress entered their environment. One is causing the other. Furthermore, before you continue to think you are somehow giving me some lesson about evolutionary processes, you need to start reading up a bit more. Shapiro says cells are sentient beings. The latest discoveries in epigentics are telling us that the genome is gathering data throughout its lifetime in a flexible manner, and passing that knowledge on to its offspring genetically through a complicate series of information storage, meanwhile you are still trying to cling on to this crazy notion of get a lucky error, wait a million years, get another one wait...without the slightest evidence to show this is possible, and with scientists now coming out right and left saying it in fact is not possible.So please save your lectures about trying to educate me, and save your lectures about manners on this forum until you do something about the one who instigates the crap. You allow Dr A to say any meaningless, snarky crap he wants ad nauseum then you say I am not following the guidelines. What's worse is that he doesn't even have the ability to formulate an interesting insult; calling people silly little men all day long? I am sure your audience must love his comedic banter. Are the guidelines as flexible as your use of the word random?This is exactly why I told you anyone with an opposing viewpoint will quickly get tired of posting here. You don't do anything to encourage a level exchange of ideas, you simply want to win your arguments at all cost, and somehow you think allowing Dr. A to just make a mockery out of civil discourse helps your side look like it must be winning.Well, it doesn't!

Random with respect to what? You need to be specific here.Is the lottery nonrandom because all of the results are always between 1 and 50 instead of any number? Is the lottery nonrandom because it always occurs on Wednesday and Friday nights?Edited by Taq, : No reason given.

Look who's talking. You have yet to define random as it applies to evolution and to these genetic systems. No one is saying that the genetic engineering systems are random. We are saying that the mutations produced by these systems are random with respect to fitness. That is, these systems produce mutations that are detrimental, beneficial, and neutral. You have shown zero evidence to the contrary. So mutations are nonrandom with respect to time. I agree. Epigenetics does not involve mutations, and epigenetics can not explain the differences seen between species. It is a non-sequitor.So I will ask again. Is the lottery non-random because it occurs at a set time every Wednesday and Saturday night (or whenever it is)?

#3: Sometimes random and sometimes non-random.#4: Non-random with an added stochastic element.#5: Random and filtered.

I beg to differ. As part of the SOS response in E. coli they upregulate the expression of an error prone DNA polymerase that increases the random mutation rate.

quote:

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PLoS One. 2010 May 27;5(5):e10862.

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Competition of Escherichia coli DNA polymerases I, II and III with DNA Pol IV in stressed cells.
Hastings PJ, Hersh MN, Thornton PC, Fonville NC, Slack A, Frisch RL, Ray MP, Harris RS, Leal SM, Rosenberg SM.

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Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America. hastings@bcm.edu

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Abstract
Escherichia coli has five DNA polymerases, one of which, the low-fidelity Pol IV or DinB, is required for stress-induced mutagenesis in the well-studied Lac frameshift-reversion assay. Although normally present at approximately 200 molecules per cell, Pol IV is recruited to acts of DNA double-strand-break repair, and causes mutagenesis, only when at least two cellular stress responses are activated: the SOS DNA-damage response, which upregulates DinB approximately 10-fold, and the RpoS-controlled general-stress response, which upregulates Pol IV about 2-fold. DNA Pol III was also implicated but its role in mutagenesis was unclear. We sought in vivo evidence on the presence and interactions of multiple DNA polymerases during stress-induced mutagenesis. Using multiply mutant strains, we provide evidence of competition of DNA Pols I, II and III with Pol IV, implying that they are all present at sites of stress-induced mutagenesis. Previous data indicate that Pol V is also present. We show that the interactions of Pols I, II and III with Pol IV result neither from, first, induction of the SOS response when particular DNA polymerases are removed, nor second, from proofreading of DNA Pol IV errors by the editing functions of Pol I or Pol III. Third, we provide evidence that Pol III itself does not assist with but rather inhibits Pol IV-dependent mutagenesis. The data support the remaining hypothesis that during the acts of DNA double-strand-break (DSB) repair, shown previously to underlie stress-induced mutagenesis in the Lac system, there is competition of DNA polymerases I, II and III with DNA Pol IV for action at the primer terminus. Up-regulation of Pol IV, and possibly other stress-response-controlled factor(s), tilt the competition in favor of error-prone Pol IV at the expense of more accurate polymerases, thus producing stress-induced mutations. This mutagenesis assay reveals the DNA polymerases operating in DSB repair during stress and also provides a sensitive indicator for DNA polymerase competition and choice in vivo.

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DNA Pol IV does not specifically target mutations in the lac promoter. It targets DNA breakage, and repairs it with more errors than other polymerases. So while the timing of the increase in mutations is nonrandom with respect to time the mutations produced by this genetic engineering system ARE random with respect to fitness.

Percy writes; Before I answer about Shapiro, I want to clear something up. I had been posting quotes from Shapiro and was told that we don't want quotes we want your interpretation.
I then scanned Shapiro and made notes and subsequently posted them with the preface: SHAPIRO WRITES.Because I did not copy and paste but rather read Shapiro's paper and typed notes which I supplied in my post.
Some of them were actual quotes, some were not. But I gave attribution to Shapiro.I then gave my summary of what I believe Shapiro is asserting.I then posted, in reply to molbiogirl in post 648 all the cites to Shaprio in my post.
Lets please drop that subject ok?

I agree, Percy.That's why I suggested shadow work on the questions with us here first.So they address the same issues, so they're clear, etc.

Good now we are getting somewhere, the engineering systems are not random.Now since you are struggling with the definition of random, let's use the Definition of Random: Adjective. proceeding, made, or occurring without definite aim, reason, or pattern.A popular synonym for random is accidental.Some popular antonyms for random are non-random, guided, organized, methodical, precise.Now hopefully we are making some headway, so let us continue. Could a system that is organized, methodical, precise intricate and with a definable pattern arise from randomness (or from an accident if you will)?Well, I suppose it COULD. We can't say definitively that this is impossible beyond a shadow of a doubt. Sure, theoretically almost anything is possible. But that would be an extraordinary event of unseen proportions. An event such as that, a methodical, precise, organized system arising by accident, well that would be so incredible that at the very least you would need implacable, undeniable evidence to ever believe such an unheard of event. Such an extraordinary claim would surely require a mountain of proof.So in lieu of such extraordinary evidence for the incredibly unlikely, we can pretty much rest assured that an organized, methodical, intricate system didn't arise by accident.And so the needle swings.

Why not just ask him the crux of the matter:Can you explain how an organized system of intelligent cells directing their own evolutionary pathways could have arisen accidentally?Or more simply, why doesn't an intelligent cell suggest an intelligent design?

I'm not the one with the problem, mate. No, but then evolution as a whole is not random or accidental. It includes natural selection. Evolution is more than just random (with respect to fitness) mutations. It is a two step, stochastic process that includes the non-random mechanism of natural selection.At the same time, we could also look at other natural phenomenon such as hurricanes that are well organized and intricate systems that arise through random interactions in the atmosphere.Also, you are now avoiding the question of whether or not the mutations produced by these genetic engineering systems are random with respect to fitness, the whole point of the recent conversation.Edited by Taq, : No reason given.

No one is claiming that they did. Why can't the intelligence within the cell come about through natural means such as evolution?

Percy supplied a quote from Shapiro at the ISCID cite. This quote is taken from the same cite. Isn't Shapiro saying these non-random changes sometimes do have an effect on the organism that are beneficial. Would that not be a non-random change that does not need a random mutation to provide adapative traits to the organism?

Thank you again, Taq."Nonrandom NGE" (natural genetic engineering) is not guided. Nor is it predetermined. Nor is it truly nonrandom. It's only nonrandom in one respect!All of the examples in his Central Dogma paper are like this too.For example, stress --> DNA uptake increases in gram positive bacteria.But the bacteria's biochemical pathway (nonrandom NGE) doesn't specify what DNA is taken up nor does it specify where it will integrate into the host genome. That's the random part.This is the original paper Shapiro cited re: this response:Claverys, J.P., M. Prudhomme & B. Martin. 2006. Induction of competence regulons as a general response to stress in gram-positive bacteria. Ann. Rev. Microbiol. 60: 451—475.And just in case anyone would like to read one of the SOS papers, I found one that's free online.Bjedov, I. et al. 2003. Stress-induced mutagenesis in bacteria. Science 300: 1404—1409.Stress-Induced Mutagenesis in Bacteria - PMCEdited by molbiogirl, : No reason given.

Well as I said, theoretically it could. But that would be quite extraordinary, so you would at least need some proof to make such a claim. Surely you would at least need some evidence of this in order to teach this as the only theory to an entire nation of science students.A much more logical and honest approach must certainly be to say that there is intelligence within the nature of a cell that we are unable to account for at this present time. Please study the problem, as all good inquisitive minds should do and keep an open mind as to how this could be.

If the results of these adaptive genetic engineerings where random, and were just as likely to cause a deleterious mutational effect as a positive one (and in fact would be more likely to be deleterious since statistically most mutations are) how in the heck could such a system persevere?That's completely illogical.