Potential falsifications of the theory of evolution

Hi Shadow,I'm replying to this message again because it occurred to me that answering this question from you might be helpful: It isn't just me who knows what Shapiro means. Many others in this thread know what Shapiro means, some at a much more detailed level than I ever will.We know what Shapiro means because he is describing the same reality as all other biologists. He can use the terms nonrandom and intelligent and sentient as much as he likes, but his choice of vocabulary cannot have any impact on actual processes and mechanisms of the real world. Anyone with the proper tools and expertise can observe these processes and mechanisms.The reason we find it so easy to understand what Shapiro really means is that ultimately he's describing the real world that we all live in and have no trouble observing. In the real world we know without doubt that reproduction is imperfect and that therefore there is descent with modification. And we know that the environment imposes pressures on organisms, and this is natural selection. At a molecular level we know about genes and DNA and how copying and reproduction introduce change and error. Everything Shapiro describes has to be consistent with descent with modification and natural selection, which is Darwin's original formulation, and with genetics, which together form the modern synthesis.An analogy can be drawn with gravity. We know through theory and have verified through empirical observations the equation by which two masses attract one another: We've known this since Newton, but though we've since discovered a great deal more about gravity, especially through relativity, all those discoveries have to remain consistent with this equation that precisely describes observations of the real world. Any discovery that contradicts this equation in any significant way has to be seriously questioned, because this equation has been known to be precisely consistent with reality in non-relativistic contexts for a long, long time.It is in the same way that we know what Shapiro must actually mean, because he has to be describing the same reality that everyone else is seeing and describing. In this reality in which we all live genetic change is random with regard to fitness. Microbiological processes are not intelligent in the way we normally think about intelligence. Cells are not sentient in the way we normally think of sentience. Nothing in Shapiro's choice of words can change what has been observed and that we therefore know to be true about reality.So when Shapiro calls a process or mechanism nonrandom we know that he cannot mean nonrandom with regard to fitness because the cellular machinery has no means of anticipating what change would improve fitness, let alone a means of making any specific change on purpose. What he means by nonrandom, for example, is the predilection mentioned before of a mobile element for insertion near the beginning of a transcription region. When the mobile element inserts it is more likely to be at the beginning of a transcription region than elsewhere. But what is the effect on fitness of that insertion? No one knows. That's because the effect is random.Shapiro also describes as intelligent this same predilection of certain mobile elements for insertion near the start point of transcription regions, but does this chemical affinity really sound like intelligence to you? And it's certainly not the same intelligence of intelligent design, which claims the microbiological process that governs this mobile element was intelligently designed. Intelligent design definitely does not claim that a chemical process is itself intelligent. It claims it was was designed by an intelligence.Perhaps the most extreme misuse of vocabulary by Shapiro is his use of the term sentient to describe cells. Sentient means conscious, aware, capable of perception. I think we can all agree that a cell is neither conscious or aware, but one could sort of reasonably argue that it is capable of perception because it responds intelligently to its environment, but when I say "intelligently" in this case I mean it in the same sense as Shapiro, who uses the term intelligent to describe processes with chemical predilections.Now Shapiro's observation that the underlying mechanisms of the modern synthesis are far more complex and varied than originally known back in the 1920's is an accurate one, but what we've learned has been incorporated into the synthesis with each little incremental increase in knowledge. This is the way all theories work.--Percy

Why would he participate in an online chat with IDists? There's only one way to find out.Now. About the wording. I suggested you outline your interpretation of his work because it will give him a jumping off point. I don't want to put words in your mouth, but it sounds to me like this is what you are saying:1. All mutation is nonrandom.
2. Natural selection works so poorly that essentially it doesn't work at all.
3. All evolution occurs due to cells rearranging their own genomes (aka NGE).
4. Cells are intelligent.
5. Nonrandom means (fill in the blank).
6. Intelligent means (fill in the blank).I'll e mail Dr. Shapiro if you don't want to. It's really no big deal.

Well, it helps if you read the papers Shapiro cites.Here's a link to one of them:Bjedov, I. et al. 2003. Stress-induced mutagenesis in bacteria. Science 300: 1404—1409.Stress-Induced Mutagenesis in Bacteria - PMCShapiro cited it in his Central Dogma paper.This is from the conclusion. Translation: Only very rarely can cells selectively generate mutations.This is the next paragraph. Translation: The initial mutations are random. Where they are inserted/where they happen is random. Then they are sorted out by the cell.Edited by molbiogirl, : No reason given.

Hi Molbiogirl, Percy et. al.I am going, pursuant to molibiogirl's suggestion, read some of the papers Shapiro has cited and then put together a e-mail to him. I will run my e-mail by you all for suggestions etc. and then send it on to him.
Busy this weekend, grandkids you know, and will get back to you all next week.Shadow 71

That's a piece of news which would surprise all mathematicians everywhere. And the makers of dictionaries. The fact that (as seems likely from your angry outpourings) you have little grasp of mathematics does not mean that you have compensatory talents in the field of literacy.Otherwise you would understand what Shapiro meant when he wrote: That is, he is correctly denying that all points of insertion of mobile elements are equiprobable; which is not to deny that such insertions are probabilistic in nature; nor to say anything remotely corrected to your irrelevant blather about philosophy --- which, I might add, is another subject which you would do well to leave alone.(I shall at this point avoid speculating on what subjects do lie within the scope of your abilities.)Edited by Dr Adequate, : No reason given.

Hide off-topic content. --AdminEdited by Admin, : Hide off-topic content.

As it seems apparent you haven't seem them yet, I'll post this note here letting you know that I posted you a couple PMs recently.

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--	Percy
	EvC Forum Director

Molbiogirl, Percy, Taq, et. al. here are the questions I am going to ask Dr. ShapiroDo you have an opinion whether random mutations per the modern Darwinian theory are the primary means of evolution today?Do you have an opinion whether natural selection per the modern Darwinian theory is a primary means of evolution today?Can genetic change come about other than by means of random mutation and natural selection?When you use the term non-random do you mean evolution can be non random in regards to fitness?When you use the term intelligent do you mean that the cells in some way are evolving w/o random mutations?Without natural selection?When you use the term sentient do you mean that the cells are capable of making decisions that affect their evolution?

I will repeat this once again. Hopefully it sinks in this time.When you say that a system is random you ALWAYS need to describe the context within which the system is random (or nonrandom for that matter). You can't simply state that something is random without describing what the randomness relates to.For example, would you say that the Powerball lottery is random? When you say that it is random, what context are you referring to? Is the Powerball lottery non-random because the drawings occur on the same nights at the same time? Is the Powerball lottery non-random because the winning numbers are always between 1 and 50 and not other numbers? When you say that the Powerball lottery is random, what are you referring to?Mutations are the same. When Shapiro refers to non-random mutations are they non-random with respect to time, to genomic position, to fitness . . . what exactly are mutations non-random with repsect to? This is a very basic question that MUST be addressed.The Modern Synthesis states that mutations are random with respect to fitness. Let me restate that again. Mutations are random WITH REPSECT TO FITNESS. If Shapiro states that mutations are non-random with respect to TIME then he is not disagreeing with the Modern Synthesis. Then you should also know that definitions in science are very precise and require context. Randomness in mutations is no different. I don't doubt his qualifications. What I disagree with is the salesmanship that he is using. Then let's try to get an idea of what Shapiro means by non-random from his papers before asking. The answers are in the paper, but perhaps not as obvious to those who are not familiar with the science. When Shapiro says that mutations are non-random he is saying that mutations are non-random with respect to genomic features and time. He is not saying that mutations are non-random with respect to fitness.For example, transposon activity is related to the state of the cell so at specific times there will be higher or lower rates of transposon mutagenesis. Also, transposons tend to insert upstream of active genes, so transposon mutagenesis is not random with respect to genomic features. However, the process of transposon mutagenesis has no way of knowing which insertions will benefit the cell. Therefore, transposon mutagenesis is random with respect to fitness as the Modern Synthesis states.

I would change it to:"Do you have an opinion whether mutations are random with respect to fitness per the modern Darwinian theory?"As to random mutations being the primary means of evolution, it doesn't make any sense. It requires both random mutations and natural selection. One mechanism by itself is an incomplete process. You might as well ask which is more important for making bread: kneading the dough or baking the dough. Without either step you don't have bread. Go with this question. I would also like to hear Shapiro differentiate between human decision making and the decisions that cells make. However, I am sure Shapiro will try to sell his idea that they are the same even though there are striking differences.

That is exactly what DNA fingerprinting is based on, the probability that another person other than the defendant will have the same STR pattern as those found in the evidence samples. DNA fingerprinting uses a panel of short tandem repeats (STR's), each of which has several alleles in the general population. For example, a single STR may have 4 alleles spread ubiquitously throughout the population. Therefore, the chances of the crime scene sample matching the defenedant is 1 in 4. By using several of these STR's you get the multiplicative of these probabilities until you get a number that is 1 in several billion. The casinos in Vegas would disagree. Their profits depend on their mathematical models of randomness. Not random with respect to what? Is the lottery not random because the drawings take place at the same time every Wednesday and Saturday? The problem is that you don't understand what Shapiro is talking about. The upregulation of DNA polymerase IV during an SOS response in E. coli is not random. However, the mutations that DNA polymerase IV produces are random with respect to fitness. You need to understand what "random" is referring to.ABE: The lac reversion via the SOS response is actually a good model for explaining randomness with respect to fitness. The earliest studies found that lac+ clones appeared at a higher rate than would be expected from known rates of random mutation. Some of the earliest hypotheses suggested that the E. coli were sensing the lactose in the environment and then producing specific mutations that would result in lactose metabolism. However, further studies demonstrated that this was not the case. The presence of lactose does not increase or decrease the rate at which the lac+ mutations occur. It has nothing to do with the process other than selecting for lac+ clones. The processes which produced these lac+ clones are completely blind to the presence of lactose. Instead, the rate of random mutation and recombination is elevated due to the bacteria sensing DNA damage.The mechanisms that Shapiro refers to are the same. They can not sense the specific needs of the cell. They do not mutate specific genes at specific bases to result in a specific function. Instead, the cell increases the random mutation rate.Edited by Taq, : No reason given.

Except this is not what Shapiro is saying, so it seems you haven't read him much. Of course he is not saying they mutate specific genes at specific locations- he is saying much more than that. He is saying it is a complete system, which deals with many levels of metabolisms, such that no one specific gene is the determining factor for any specific change. It is a much more complicated, and orchestrated mechanism. The cell is NOT simply increasing its random mutation rate. That is absolutely false.Can you image what the detrimental effects of an organism increasing its 'RANDOM" mutations would be? Remember we are talking random here (as in the mainstream WORD, NOT the mathematical concept or symbol-surely you can get this distinction). If an organism were to simply start increasing its random mutation rate-where would the net gain come from? You would have every possible type of detrimental mutation arriving in the population. You seem to be suggesting that the more "random" mutations that would occur the better the chances of survival would be, but as I have already pointed out, the OVERWHELMING majority of these mutations would obviously be detrimental (now you can talk about random in a statistical context if you wish). If every type of mutation is equally likely, why would you ever expect this to be a winning formula? Organism would be receiving lethal mutations left and right, so you would quickly expect to see a decrease in the number of viable organisms, not an increase. As the numbers decreased, likewise your chances of having the organisms that got lucky enough to have a useful one would decrease.It would be as if you had a new contagious disease enter the premises of a large factory of quarantined workers, and you didn't have a cure yet, but you had a big warehouse full of chemicals for making medicines. So you told everyone in the building, all 1000 people to just start eating all the chemicals around, and hopefully one of you will stumble upon one that is useful. In the meantime most everyone who ate the chemicals would die from ingesting the wrong toxins. Maybe someone would get lucky eventually, and eat just the right mix of things, but that would be extremely inefficient, and very unlikely.We are not seeing extreme inefficiencies, we are seeing extreme efficiencies. The organisms he is talking about aren't experiencing rapid declines and sudden drops in the fitness levels of the population as one would expect from your scenario, they are experiencing rapid adjustment and adaptation.Your premise just doesn't stand up to reason.Sidebar: I highly object to my last message being hidden. It either deserves to stand, or else everyone of Dr. A's posts deserves to be hidden. I declare solidarity with the freedom fighters. I support the right to protest. Edited by Bolder-dash, : No reason given.Edited by Bolder-dash, : In the name of freedom and justice.

That is what the research says that he cites. Then mutations are random with respect to fitness. The fact remains that the mutations produced by these systems are random with respect to fitness. The fact that morphological change is due to different mutations in different genes does not change this fact.You also claim that it is not a matter of the cell increasing it's mutation rate, and yet I cited a paper that demonstrated exactly that. Mechanisms cited by Shapiro, such as trasposon mutagenesis, have likewise been demonstrated to be random with respect to fitness.To go back to the lottery example, no one is claiming that the machine which mixes and selects the ping pong balls is the product of randomness. It didn't form by a tornado tearing throuhg a junkyard. However, the results that the machine produces are random with respect to the tickets. I stated that the chances of finding the beneficial mutation needed to overcome the overwhelming environmental stress would be higher, but it comes at a cost. The cost is the accumulation of more slightly deleterious mutations. However, a higher background of deleterious mutations is preferrable to outright extinction, wouldn't you agree? Obviously, it does work as the paper on the SOS response in E. coli demonstrates. If your life depended on getting the winning lottery ticket would you buy one or buy as many as you could, not caring how many of those tickets are losers or how much debt you would rack up? If the alternative is that everyone dies from the disease anyway, why not give it a try? Please cite examples with reference to mutations. You seem to be switching between cellular function and the process of mutation at will with no reason. Show us an example where a specific environmental stimulus evokes a specific mutation, and only that mutation, each and every time. Anything short of this is an ineffecient system, is it not? And this adjustement and adaptation occurs through random mutation followed by selection. For example, Shapiro writes:

quote:

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The adaptive benefits of this regulatory capacity are clearest in the cases of DNA changesintegrated into the regular life cycles of organisms (our immune system is an example), but biological utility is also evident in the ability to stimulate variability under conditions where proliferation or survival are threatened.
Letting Escherichia coli Teach Me About Genome Engineering | Genetics | Oxford Academic

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He is talking about the stimulation of variation, not the stimulation of specific adaptations to a given stimulus. Another key quote from the same paper:

quote:

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These systems have the capacity to reduce the size of
the genomic search space dramatically and to maximize
the chances for success by using a combinatorial process
based on existing functional components.

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So what does it mean to reduce the search space? He means favoring one type of random mutation over another. In this case, the propensity for the cell to shuffle exons and transcription units. However, these changes are still random with respect to fitness. What Shapiro is saying is that the genetic engineering systems produce mutations which have the best chance of producing a novel function, but obviously chance is still an integral part of the process.

Thanks Taq, your suggestions are appreciated. I will use those questions.Edited by shadow71, : No reason given.Edited by shadow71, : No reason given.

As you've been advised countless times, the thread where one brings discussion problems to the attention of moderators is Report Discussion Problems Here 3.0, and problems with moderation are not open to discussion. I suggest PMs.Please, no replies to this message.Edited by Admin, : Add quote.

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--	Percy
	EvC Forum Director