cypress

In other words there is indeed a relationship as I said but that relationship is not one to one at any particular time or for any particular cell. Yes, I am also aware of that reality. Again I appreciate your desire to be precise and to ensure that I understand.

I don't understand what you are asking for then. In the Lenski research the ecoli which is able to metabolize citrate in anaerobic conditions underwent a two or three step mutation and was able to metabolize free citrate in an oxygen rich environment. It was a modification of existing function due to a change in expression controls. Is this not a substantive change that was selectable? If it was then my definition seems to be consistent.

The problem isn't that it's an analogy, it's that it's a fallacious one.

 

And to answer your question, yes, I do think there is a "reasonable" probability, though treating the rise of life as one event and calling the processes "random" are both misleading.

Then you don't believe chance alone was involved and you would be hard pressed to make a case that the argument is fallacious because you reject the premise of chance alone. I don't see any reason to argue a point you don't accept in the first place. Hoyle's analysis applies to those who falsely stipulate chance alone.

And no, I don't know exactly how it occurred. Nobody does. We have some plausible hypotheses about many of the steps. An appeal to ignorance would be suggesting that because we don't know what happened, X must have happened. I'm not doing that.

No you reject the chance only hypothesis. my statement on an appeal to ignorance applies to those who pitch the chance only hypothesis.

Also functional proteins are not rare at all. Synthetic biology approaches demonstrated that synthetic peptides with more or less random elements of alpha and beta helices (IIRC) have the potential to catalyze simple reactions. Albeit with far lower efficiency than those that have arisen during evolution, of course. The existence of protein families and the prevalence of certain proteins is just another indicator of common evolutionary origins.

I find this argument to be very weak. One can use almost anyheavy solid that is denser than water for a boat anchor. Molecular biology confirms that the great majority of functional proteins are components of five or more multiprotein systems. Cherry picking exceptions does not impress me.

And as Sisyphus pointed out, no-one argues that there was just a random event and oops there is life. There must have been conditions that favored the existence of simple self-replicating biomolecules as a first step. Or maybe there were several first steps, so to say. Arguing from ignorance is not helpful.

I appreciate that you seem to be retracting your earlier implied argument about chance systems (where you took exception to Hoyle's indictment against chance alone) and have made clear you are with the rest of us who, like Hoyle reject that chance alone might have generated life from non-life.

This is not a "side issue." If "substantive differences" just means "difference in genome, whether good, bad, or neutral," your figure no longer supports your claim. 10,000 genetic changes could easily be accumulated over thousands of years, even if you argue that 10,000 significant beneficial adaptations could not be.

 

Could you stop dodging the question and just answer it? It'd be much easier than continued quibbling.

Skeptic asked the same question and I answered it several posts ago. Substantive changes are function and form modifications and new function or form subcompontents that were incorporated into the entire population. this disposes of ChardonY's 2nd point. I am also speaking of population effects which disposes of the first point. The third point does not explain or demonstrate how natural processes actually derive digitaly encoded functional information faster than a blind search so it is irrelevant either way.

Marat's argument is interesting but it is a just so narrative without a causally adequate process and is as meaninless as pure speculation. Could haves and would haves, ifs and ands.

Wait, I think that if you want to point out a 4 order of magnitude difference then you can't discount the 6 order of magnitude difference that I pointed out earlier -- humans have ~1000X the DNA and ~1000X the mutation rate as compared to bacteria.

Sure but the analysis already accounted for that. My previous description skipped past the math and took shortcuts and simplified and estimated to avoid what I considered too much detail to make the post more brief. Perhaps we will need to go into the details. If so I will start a new thread on this too.

We've already tested this and found it false. The simplest example is the reversal of SNP mutations, where a random process creates a functional protein from a non-functional protein, and a non-random process favors the bacteria with the more functional protein.

As I have previously acknowledged, we do not lack examples of mutation generating function in one to three steps which is in the realm of what a blind search can accomplish, what we lack are actual examples of the multistep evolutionary pathways the theory predicts exist.

It's very much the key. If your "substantive differences" mean "significant alterations in genome," regardless of what functional advantage or disadvantage they bring, or whether they're neutral mutations, then the objection that major adaptations do not occur fast enough doesn't fly. All one needs is a mutation of any kind, not just a beneficial adaptation. And I think you'd agree that it takes many mutations to generate one beneficial mutation.

Whether I object or not is not the issue. Nor does it matter what I agree. The issue is that when experiments are conducted and numbers are run, known and observed natural processes including evolutionary processes simply do not generate this kind of information at a rate consistent with observed diversity and estimated geologic time. This is a fact that cannot be hidden in back of side issues.

Is it? I thought you were talking about Fred Hoyle's analysis, i.e. "Hoyle's Fallacy." That is about specific complex structures arising by chance simultaneously.

This is a different issue I think. You suggest that Hoyle's analysis is faulty simply because it uses analogous biological structures instead of actual ones because we lack the data required to use the structures that actually were involved in generation of the first biologically active self-generating system. Scientists use analogies all the time. Should we dismiss them because some people don't care for the analogies? It illustrates the point and it addresses one proposed mechanism directly. If you have a better set of components to illustrate the issue than the minimal set of proteins, lets have them.

While we are at it, let's make sure you are actually arguing a counter point rather than making an appeal to ignorance. Do you claim that there is a reasonable probability that life arose from non-life by random chemic processes alone?

The vacuole membrane is also denatured by methanol and this makes sense since the vacuole holds waste products and thus the mechanisms across the two membranes should be similar and affected by the same chemicals.

Who is suggesting that fully functional life as we know it would appear suddenly and spontaneously? Is that how you're interpreting "arise by chance?" The rise of life as we recognize the term would be a many step process, and those steps would not have to (and in fact probably could not) happen simultaneously. The "lightning hits bowl of goop" type origins of popular imagination and common straw man do not resemble anything scientists are actually investigating. The origin of life is still mysterious and hypotheses are incomplete, but such as they are they're a lot more plausible than that.

I don't know of any informed individual who makes the suggestion that life as we know it appeared suddenly by chance. I do know of many who suggest that random processes generated the first biologically active system we would describe as life-like and it is this suggestion I and the names I provided dismiss.

Yes especially at the start. But odds are it wouldn't fit on the phylogenetic tree -- we'd have no trouble mixing and matching proteins from distantly related species, like we do now adding Green Fluorescent Protein everywhere. And if projects like Folding@Home progress well, we can start designing our own proteins or optimizing existing ones.

An interesting aspect of proteins is that generally the primary sequence does not determine function, what generally does determine function is the shape and chemical and spacial affinities of key active areas (binding sites) of the protein.

And the adaptations I listed outperformed and out-reproduced the others, since they became the dominant traits. The entire average population size, shape, and growth rate changed. These adaptations were found to be beneficial when compared against pre-mutation cells.

 

Additionally, Lenski noted beneficial alterations such as the loss of the ability to grow on ribose, as a result of a gene deletion, and mutations in the spoT gene, which provided a significant advantage to 8 of the populations.

They survived along with the other variations and became diluted in the population unless purposely isolated. Hardly the model that is described by the theory. But even if I were to accept all 20 as examples of selective advantage the 5+ order of magnitude gap has closed by less than two orders of magnitude so we are arguing over an insignificant difference.

We observe mutation rates changing. Because mutation rates change, assuming that they have stayed the same in the past is naive. Lenski in particular observed that adaptation rates slowed after thousands of generations, likely because the bacteria were becoming well-suited to their environments.

 

If you are going to discount several key predictions of evolutionary theory -- punctuated equilibrium, variable adaptation rates, and so on -- and then complain that it doesn't work anymore, well, that's your problem.

 

Also, your definition of "science" is inaccurate. Science merely requires testable hypotheses. "Mutation rates change" is testable. Most creationist speculations cannot be tested by definition -- an omniscient designer or god can not be tested for in an experiment.

I don't discount the variation, since any change in mutation rate in the lab experiments figure into the results, that factor has been included. Your hypothesis is far more than "mutation rates change though, yours is that higher mutation rates in the past account for the observed gap. Significantly greater mutation rates (the several orders of magnitude needed) won't help anyway. By Genetic population models, as you significantly increase the mutation rate the number of catastrophic mutations overlap with any neutral and beneficial mutations so that any pathway that otherwise would emerge is cut off. Besides if significant changes in mutation rates were observed and were advantageous then Lenski's research would not be the one we used as an example as that research would show better results. Your claim that mutation rates in the past could account for the gap not only seems theoretically incorrect, it does not seem to be testable.

My hypothesis is testable. It is that we observe that biological systems contain large amounts of digitally encoded functional information. We also observe that mind/intelligence is the only causal entity that generates large amounts of this kind of information. Therefore an agent with a mind/intelligence likely generated life. We test this by conducting experiments to see if natural processes do generate this kind of information and we observe genetic engineers closing in on the task of generating new life forms by design. My hypothesis does not make any appeal to an omniscient god. However this is evidence that suggests.

The key is what you mean by "substantive alteration." It could mean "mutation in genome of any kind," it could mean "added feature," it could mean "beneficial adaptation of any kind," it could mean "only added features of a certain size," or just about anything else. The veracity of your claim depends on your definition of "substantive alteration."

No it's not the key. Regardless of how we define terms, observed evolutionary processes simply do not generate large amounts of digitally encoded functional information any faster than a blind search. Artificial selection (captive breeding) does however, but even it seems to have limits. Only genetic engineering is known to bridge the gap. We can sit here and quibble about the finer points but none of it will change the outcome.

And Cypress, you were first talking about gene expression. You do know the difference from what is being asked and discussed, I presume?

There is a relationship between gene count contained in an organisms genome and the quantity of genes expressed, and I understand the distinction. Thanks for your concern.

And I suppose you do have good references for these assertions? I mean, ideally more than the opinion of an astronomist who has more than a fair share of controversial views?

Good in the sense that alternative estimates are not clearly better. P.T. Mora a Research Biologist at the National Institute of Health provided a critique of the chance hypothesis for life from non-life back in the early sixties in published in Nature. That assessment was very similar to Hoyle's. In addition Robert Shapiro and Francis Crick accepted the probability of life by chance was effectively nill also. I find that those who suggest that life arose from non-life by chance are simply concealing an appeal to ignorance in a chance wrapper. If you believe I am wrong about this, by all means suggest a different number a we can discuss the relative merits.

Well, when we start designing our own life forms, then you can expect to find something that won't share half their genome with all other life.

Given the relative rarity of functional proteins, I would expect that very few of the genes in artificial life will be unique. I would expect that most will be reused from the pool of known and functional proteins.

Put me down for skeptical.

This is a false analogy. Lenski's bacteria were not subjected to selection pressures (they were grown in their ordinary environment), they were pre-adapted to their environment, and Lenski had no way of detecting other mutations and alterations that may have been substantive but not immediately visible.

They were under selection pressure with oversupply of citrate in an oxygenated environment and limiting supplies of nutrients readily metabolized.

(For example, a mutation could have occurred that set the stage for a later development, but did not cause significant changes in the bacteria by itself.)

Speculation. Ifs and ands, but hardly scientific.

Furthermore, your claim of "1 substantive alteration" is false; Lenski has noted numerous differences between his lab bacteria and the "original" bacteria, such as significantly increased size (a doubling in volume), a change in cell shape to a more spherical form, a decrease in reproduction rate (as the larger cells consume more resources and compete with each other), and a change in DNA repair which accelerated mutation in some of the populations (evidently as a way of speeding adaptation). Lenski himself estimates 10-20 beneficial mutations that became fixed in the populations, among numerous neutral or deleterious mutations.

Estimates are fine but only one is documented by the normal measure what the theory of natural selection predicts, and that is the ability to outperform and out-reproduce relative to the others. The model for evolutionary algorithms is always to kill off the weakest for a reason. Only the one alteration significantly outperformed the others. The rest of these changes did not outperform the rest of the population. Sorry, it is not proper to move the goal post. I repeat, just one significant alteration.

Furthermore, it's silly to assume that there'd be one fixed mutation rate that would occur over all time. The evidence for punctuated equilibrium suggests that it is responsible for a significant portion of evolutionary adaptations, and one would not see punctuated changes in a short-term sample without being extremely lucky, or introducing the bacteria to significantly different environments.

Science requires citation to processes currently in operation. We observe a narrow range of mutation rates today, anything different than that is speculation. If speculation is allowed in this debate then let's also allow the creationists their speculations.

Finally, I'd like to see a source for your numbers, so I can see that "substantive alterations" in the genome means "significant beneficial change in phenotype", rather than simply "a difference in genes."

There are several estimates based on extensive study of differences between modern humans and modern primates. There are hundreds of millions of point level differences and even a few thousand unique gene sequences. Is it hard to believe the estimate? It may take me a few hours to find this the source material and confirm my estimate, so can you indicate what number you believe is correct? If we are close I prefer not to quibble over a side issue since this will not change the substance of the primary point which is encoded functional information and the inability to demonstrate if natural processes do generate it. How many substantive alterations would you accept as reasonable? What about from say the first mammal to modern humans?

Lenski estimated 10-20 beneficial mutations, but the number of neutral mutations -- which would not be easily noticed -- could easily be far higher in each population. And, of course, Lenski did determine the mutation rate per base pair in the bacteria, which could tell us the number of "substantive" mutations of the genome, whether they're beneficial, neutral, or unhelpful.

Lenski's definition of beneficial seems loose as does your definition of substantive. Neutral mutations don't eliminate options and thus do not change information content.

(Also, I don't see how you can make the claim that human and bacteria mutation rates should be similar, when their environments are significantly different, they are subjected to different selection pressures, and their molecular mechanisms for repairing DNA damage are different. Lenski observed a change in mutation rates after 20,000 generations in some populations; why should humans over 200,000 generations maintain the same mutation rate? Why should bacteria over tens of thousands of generations? It's a very naive claim.)

Have a look at the lab notes regarding the change in mutation rates it appears to be isolated cultures where mutation caused damage to critical replication components. Note what happens when these strains are made to compete with slower mutating lines. We don't know if human ancestors had different mutation rates, we can only go by the processes and rates we observe today plus what we know about the mechanisms that lead to faster rates and it does not seem encouraging for your position. I find it even more naive to use speculation to prop up a untenable position.

If you're going to make claims about evolution's observability, at least familiarize yourself with the results of experiments already conducted and understand the mechanisms explained by those experiments.

That's just it, I seem to be quite informed about what Lenski's research shows and what it doesn't show. We only seem to get into contention when either Lenski or you want to go off and speculate about what things might mean or might have been.

Returning to the primary point, experimental results (and Lenski's seems to be among the most optimistic available) we have documented evolutionary pathways where selection is actually selecting an advantageous mutation only once and then the pathway is just three steps long with one neutral or detrimental step. This pathway fits within the range of what one would predict from a random walk so we have no example of known evolutionary processes deriving functional information beyond what little is predicted by information entropy. With this, it seems clear to me that naturalism is in need of a new and improved process in order to explain life and the diversity we observe.

But, if we're not looking at how surprised people are at the DNA, it becomes obvious that mutations can create information as well as modify or destroy it.

 

I shall now give the example I thought of, that would result in an organism evolving a series of 4 new functions each dependent on the previous new one, with a population and timeframe amenable to a science experiment, the example I said you would not accept. It is thus: take an organism, and identify within it a series of 4 proteins in a metabolic pathway that is important but not vital. Ideally, each protein provides a useful function even without the following proteins. Next, identify a location where a single nucleotide mutation will disable each of the proteins. With this as the starting organism, place several colonies of them in a growing environment and let them evolve. Several colonies are needed to be certain this works, as it is chance based. I have no doubt that they will evolve to gain 4 new abilities each dependent on the previous.

 

Now, you will dismiss the above, claiming I "cheated" by inserting the information ahead of time. However, think about this some more. Are you going to say that a functional protein has just as much information as a useless protein? Are you going to say that evolution added some information, but not very much? Or are you going to say that getting 4 specific mutations among trillions of tries is unlikely?

Sounds hypothetical. Is this a real event or a just so story?

The truth is, DNA contains zero communication-information, and evolution cannot add any more communication-information but could destroy some if it were there. Nobody cares. The context of the data on the DNA is cell mechanisms, not communication.

Not so. It fits the definition of encoded functional digital information in every sense. It has both semantics and syntax. It is translated and transcribed. It is independent of the material it is encoded on. The messages are independent of the carrier. The ratio of functional to non-functional messages is very small 1 in 10^74 by our best estimate.

Several things. First, bacteria have less DNA and a lower mutation rate than humans (1000 times less DNA with mutation rate 1000 times lower). Second, you're not counting the human's rate of death before birth, which is fairly high in the past but also plays a role in evolution, so the population is somewhat higher than you expect. Third, can you give me an example of one particular substantiative difference of that 10,000 (and not a multi-gene difference). I ask because I had understood your demand to be significantly different than this sort of difference. Fourth, there were several additional differences in the Lenski experiment bacteria, some of which could be noticed by Lenski himself and some which would have been invisible to him, as Cap'n noted.

I addressed most of this already, but I add that none of your objections substantially change the result. We can quibble over the numbers and still fall many orders of magnitude off the mark.

The point is not that history can tell us what happened, but rather that evolution predicts this historical data and the probability of making consistently correct predictions on such a large dataset is absurdly small -- and so the probability of the theory being correct is taken to be very large. This is little different than in other fields, although in this case the larger dataset is historical and fresh data can only be gotten slowly.

The evolutionary tale fits the historical record because it has been carefully molded over 150 years to fit it. Now with modern experimental techniques its ability to morph is falling on hard times. If we apply scientific rules to the predictions by requiring citation to observable processes it falls way short of accomplishing what is prescribed to it in the timeframe assigned. We simply do not observe evolution generating functional change at the required speed. It does not generate new information any faster than a random walk. In other words the fitness function does not appear to contain smooth pathways from one functional advantage to the next. It appears that there are discontinuities that limit the traverse. That being the case we should be looking for alternative processes.

You have offered a number of hypothetical examples of how evolutionary processes might generate this kind of information but it is all presupposed or imagined. We know that a mind generates this information. My point in going down this path was to demonstrate that those who claim that known evolutionary processes do generate new function and form are unable to offer known examples, instead they show that diversity happen by comparative analysis and they presume that it happened a particular way without knowing if it did or not. You have taken this same tact.

Yet information has consistently been on the increase, both in our society and genetically by looking at the number of species, in the latter only being reduced during periods of mass extinction. I'm not buying it. To which experimental analysis are you referring?

Of course it has. Life had a beginning and diversity happened. The question is how? Information has increased over time, but how? You presuppose the answer is by natural processes but I have shown that thus far only mind is known to be capable of generating the quantity of information required to begin life and allow for its diversity. You have offered only hypothetical imaginations of how known natural processes might do so. Personally I suspect there is some group of undiscovered processes that account for generation of functional information at a rate sufficient to account for diversity of life but at this time, mind is the best explanation for life and the universe and perhaps even diversification.

Unless there is some real example of natural processes in operation today that can be demonstrated actually generating large amounts of information quickly, I don't see much point in continuing this discussion. We have gone down many rabbit holes and chased many a goose and we have come away empty.

No, I'm not talking about my own mind but rather of context. I intend to show that given a certain context, any data string could be significantly valuable information, whereas in another context it may be worthless. Thus, communication-information depends not on the data but entirely on its context -- and as such, it is impossible to measure for anyone who isn't omniscient, and worthless as a measure of information without assuming things about the context.

You are suggesting that every mutation is functional but Douglas Axe and several others have already shown that this is false. The ratio of functional to non-functional expressed sequences seems to be less than 1 in 10^74

If I understand your sentence, you are saying that everything you have just told me contains no information, since it does not generate a functional system. My measure of quantity of information is approximately the size of the data when it is as compressed as possible. Function of it or lack thereof has nothing to do with any particular string of information, since there is no difference between useful and useless information, not without looking at the context.

 

My invitation to suggest a string of data that you believe contains no information is still standing.

I can only conclude you don’t understand my position. Like many things, information takes on several forms. We are focused on a particular kind of information as I have defined. I am being specific about the kind so we avoid confusion. These sentences also contain and convey information by virtue of the fact they eliminate vast quantities of alternate possibilities, however in this conversation I am being more specific. Functional information is information that when processed results in a functional system. Data is different from information because data requires analysis and interpretation in order to derive meaning and thus eliminate alternatives.

I understand your definition of information and I accept it for what it is. It is a very broad definition that is useful in data and information transmission especially in that the compressed instruction set is information since when it is processed, the original sequence, or a representation of it, is regenerated and thus alternative configurations are eliminated. I don’t find this kind of information applicable to biological systems and thus making a comparison to it makes little sense. However, the compressed instruction set is information and I do not know of any example where random processes are able to generate the compressed representation of a particular sequence, irrespective of the source of that sequence.

On the contrary, we have identified several. The metabolic pathway of glucose is a good example.

Is it? You can describe the stepwise evolutionary pathway that derived the components, expression controls and developmental controls for glucose metabolism from a system that lacked it?

No, what you are asking is that we observe an event which the theory predicts to be unlikely to happen within the confines of a lab within a reasonable amount of time, and then pretending that is evidence against the theory, or that it is a reasonable suggestion and you remain open-minded.

Nonsense. Let’s test your claim with what the theory predicts about human evolution and compare it to the lab. Human history is estimated at 6 million years. The human genome contains at least 10,000 substantive differences from the predicted primate like ancestor. In 6 million years that is about 200,000 generations, and thus about 20 substantive alterations per generation amongst fewer than a trillion cumulative population . In the lab Lenski’s ecoli work alone has covered nearly 35,000 generations with over a million, trillion cumulative population and he got a total of 1 substantive alteration. The prediction would have Lenski getting several orders of magnitude more and this is only one of the thousands and thousands of relevant lab experiments being conducted to observe evolutionary processes. By this example it should take just a few years to confirm the presence of evolutionary pathways by noting and comparing the rate that these pathways precede as compared to the rates required by evidence from the fossil record. By Lenski’s example and others including several focused on applying observed rates with population genetic models, it is clear that the rates are orders of magnitude too slow. Your claim falls flat.

In this your demand is far more close-minded than my demand to see someone raised from the dead, since the latter is something that not only has (according to the Bible) happened about 5 times in a few thousand years but also that only requires a little bit of faith the size of a mustard seed for anyone to do.

Please don’t exaggerate. My request is far more reasonable as I demonstrated above and furthermore unlike yours, it allows you to cite observations of process known to exist and in operation today.

But why the need to do it the difficult way? Why the requirement to observe something which the theory itself predicts you could have to wait millions of years to observe (really, the odds of an ability sufficiently novel to satisfy you, and on top of that for it to happen to the same species limited to a minuscule population (1 ton would be like 0.00000001% of earth's biomass) within a literal blink of an eye (0.000001%) of geologic time, and if you wanted them to build off each other than it has to relate to 1 out of thousands of genes three times, which would be a chance of 0.0000001% of a chance if you wanted 4 such examples and the four did happen anyways within the lab population and experiment runtime. Why such an unlikely thing, when you could simply look at the historical and DNA evidence?

Nonsense, historical and DNA evidence cannot tell us how the similarities and differences came to be the way they are, a prediction that cannot be verified is of no use. I am asking for just a handful of observable modifications. Protein-protein binding sites are generally made up of 5-10 amino acid loci. Likewise for expression and developmental controls. Protein shape is determined by folds, which are also based on binding sites. All of these are the lowest level functional precursors to novel form and function. I am not asking for development of an entire system I am only asking for evidence that random error and selection generates these lowest level subunits. Based on population genetic models these would need to occur every few hundred generations, but even after over 35,000 generations of observations in ecoli and 50 years of observing malaria with countless tens of thousands of generations and trillions of trillions of organisms (10^15 times as many as the total number of mammals that have ever lived) still no example of a new binding site

Like the Bible, evolution makes specific predictions as to what DNA should look like. According to the Bible, DNA should look like the quantity of DNA that fits on a big wooden boat, and the maximum number of alleles depending on the type of animal -- 4 alleles per unclean animal, 14 alleles per clean animal or bird, and only 1 allele in the Y chromosome and only one type of mitochrondrial DNA for unclean animals.

The bible is not a science manual. Are you suggesting that science is similar to religion? If not, perhaps you should use a better example. For the record I have not once suggested that the Bible provides an accurate representation of how life diversified.

Evolution predicts that DNA will look like it was copied and mutated, with less mutations to the more vital genes due to natural selection and probability of improving an already well-refined gene, and more mutations in neutral DNA. Guess which one turns out to be true?

Turns out neither are accurate. I would not expect the Bible to be accurate on these issues but I would expect a valid theory to be accurate. The number of exceptions to this model are staggering. Take the gene that codes for histone IV for example. It is highly conserved with fewer than 6 of its hundreds of nucleotides showing variation between a very diverse group of species. Your model predicts there should be strong functional constraints (vital as you call it) but lab experimentation in yeast cells confirms that the constraints are mild. Several mutations do not alter fitness by any measurable amount. Even more astounding are the thousands of ultra-conserved elements (UCE’s), these DNA segments, hundreds of base pairs long are found across a wide range of species.

This is quite obviously false. Many times in evolutionary history genes have been copied wholesale, and then one of the copies modified to a new purpose. This does not destroy the original information.

Perhaps you misinterpreted what I said. Duplication and then modification can increase information but this in direct observations, this is rare relative to the losses occurring by other mechanisms. Since historical analysis can only provide measures of similarity and differences but don’t provide objective measures of the various mechanisms nor any information about processes we can’t use it to derive meaningful measures of information gain or loss. Experimental analysis indicates that on average information does not accumulate. This is as we would expect from information entropy laws.

When there is no difference between two things it is reasonable to say they are identical. So yes, I do consider any string of data to contain information, though you are welcome to try to show a string of data with no information (again though, I shall be the one to put some context to said string).

If you are putting context to the data then it is your mind that is deriving information based on the data string. I am quite aware that human minds are capable of deriving data and don’t see any value in this demonstration. I will stipulate now that your mind can generate information in the process of analyzing any data stream I was to provide. However this is quite different than encoded digital information that is translated, transcribed and then processed by chemic processes (without a mind) to derive a functional system.

What would this upper limit be? i see no reason to think there is an arbitrary upper on the genome of any organism.

 

http://en.wikipedia.org/wiki/Genome

As you and skeptic suggest, arbitrary was a poor word choice. Variable might have been better since it depends on many of the factors mentioned by other posters. As far as where this limit lies for any particular organism given the environmental conditions, I don't have enough data to say.

Considering that life arose by chance, it sure is a perfect system for the microbial community. This is evident in the fact that they have always been here.

Most origin of life researchers reject the notion that life arose by chance and for good reason too. The probability of deriving biologically relevant systems by chance processes is estimated in excess of 1 in 10^41,000 even by the more favorable chemic processes by numerous calculation methods, one of the more rigorous was by Sir Fred Hoyle. Current research is focused on self-assembly processes but thus far these are not faring any better.

Perhaps you meant to use the word "assuming" rather than "considering".

Biological processes in general are functionally efficient. Controls that regulate gene expression tend to switch of expression of non-functional genes and this imposes an artificial and somewhat arbitrary upper limit on the quantity of expressed genes in organisms.

Very well then, it seems "information" seems to be our main point of contention. If you can give even one example of a random string of data that has no value of information, while allowing me to provide context for said data, I shall change my mind. On the other hand, if I can demonstrate that any arbitrary string of data will have value as information with a given context, then I would expect you would change your mind. Sound fair?

No I don't think so. Your use of the term "value of information" seems altogether different than "coherent digitally encoded information that when processed generates functional systems". Did you intend to change the meaning?

On my part, I apologize for some of the ridiculous "demands" I have made, although I am sure you realize those were more of a rhetorical device, examples of why your demand could be seen as unreasonable and most definitely didn't prove anything. While I cannot read minds, I am 99.9% sure that you would change your demand were I to give you one example fitting that description that I can think of.

I recognize that you were attempting to make analogies, but I consider them to be misapplied. I am also somewhat disappointed in your lack of trust. Unfortunately we will likely not face this issue because there are no such examples. The neo-Darwinian narrative of gradual change over time predicts millions upon millions of these pathways and yet we can identify none. How odd.

Also, it really makes no sense to claim that natural processes cannot generate information, since the information produced by evolution is both observed and encoded and digital, as you requested.

It makes a great deal of sense because we don't know of any evolutionary process in operation today that is observed to have generated any significant quantity of new information required for new form or function beyond what little can be shown to be derived by a blind search plus the probabilistic resources available to search shape and chemical affinity space using population genetics modeling. It is a tautology for you to presuppose that there exists such a process. If observations of known processes existed then you would be able to provide an example of one of these multistep evolutionary pathways we discussed. Again let me remind you that research has not yet identified any pathway greater than three steps but we need pathways in the millions of steps.

Similarly with fine-tuning, evolution is a natural process that can produce organisms fine-tuned to an environment (which has also been observed).

Once again I must correct you. We have a metaphysical belief but we do not know if natural process produce new organisms. We do know that evolution can generate adaptations of pre-existing function but these adaptations on average destroy as much or more information as they generate. Adaptations tweak the dials within the range minimal range of survival but they must be in that range to begin with for adaptation to work.

Of course, since I'd also consider random data to be information, I think it best we work that out first.

Yes we should, but first we need to adjust the criteria for what constitutes the kind of information we are talking about. If we relax the criteria enough we can describe nearly anything as information.

Has science provided any explanation as to why our DNA is 10 to 1 in microbial DNA. What use does it serve? It gives you the impression that we are a species of colonized bacteria. If this is true why did they not just make all life look the same since they are viewed as mindless biochemical machines/germs etc. If are just mobile food processing machines that aid in preventing their enemies from invading our bodies, why bother giving us this illusion that we are unique?

If you look at the research more closely what you will find is that by some percentage estimated between 10% and up to 90% of the expressed sequences that generate proteins share a degree of similarity to protein sequences in microbes depending of course on how you account for unique protein sequences. similarity to other species display a range of values for the same reason. If you don't include unique proteins with no corresponding function between the two species being compared then the percentage is high, but if you do include them the percentage can be much lower. The degree of similarity is also somewhat vaguely defined in that the cutoff for what constitutes similar is somewhat arbitrary. It is this similarity that leads to a conclusion by induction that gene sequences in humans have microbes as the original source.

Good point. So what would we have then? It would depend again on how the designer used the random numbers. Would we have the computer making unconstrained free choices? No, it would react in accordance with the rules prescribed by the designer and the results would be random with constraints. The computer and code is passively delegated the constrained range of outcomes to a random generator. We now have an example of a designed system that generates outcomes based on design, necessity and chance.

Computer programers sometimes choose to use pseudo-random number generators that are deterministic in their code to add a degree of variation and complexity because the range of inputs is great so the range of output can be as well. However, there is no contingency in the outcome of these functions. They are as deterministic as every other computer function.

It seems that rather than having misunderstood my position, you are employing the tactic known as "begging the question". I've said the algorithm has information (all algorithms do, by the way). And you assume that the presence of the information is proof for a designer -- the very thing under dispute. First prove that the presence of information proves a designer, and then you can speculate about evolution being designed.

From the beginning I have been speaking of evidence as opposed to proof and if you read my posts you would note that I am not assuming this is proved. The questions I asked were rhetorical to help illustrate how I believe your complaints were misplaced. Uniform experience and observation confirms that intelligent agents generate coherent encoded information but there are no confirmed cases of natural processes accomplishing the same. This is evidence but since alternatives are still in play, it is not proof. If you believe that my statement is incorrect and that natural processes do generate coherent information then let’s discuss it. Otherwise the minor complaints you raise are side issues that I don’t think need to be discussed any further.

Perhaps this is a language issue. I consider any random string of data to be information. Because it is. If that random string had value of some kind for any reason, then it would just as clearly be information as would a string of data that the value of could be seen easily.

Random strings of data is .... well.... data so there is no reason to redefine it as information. If random strings “had value” in the sense that it could be processed to produce functional systems, then it indeed would be information in the sense I mean. Do you have any example of random data containing large amounts of this kind of information capable of being processed to produce functional systems?

You seem to have a more restricted view of what information is, but I don't know what yours is. If this is indeed our point of disagreement, I could expand on it further, and I would ask that you define what you mean by "information".

I am speaking specifically of encoded digital information such that when processed generates functional systems. Computer code is an example. Instruction manuals are another. The information encoded into DNA is a third example.

Right, but what would it prove? Even were I to give an example, where 4 consecutive new abilities were evolved within a reasonable time while being observed, you would simply change your demand.

Would I? Do you read minds? I have asked for this example because the inability to produce one is confirmation of the claim I have made. If you produce an example then I will have to retract my claim that random error and selection does not produce novel function and body plans within the available geologic timeframe.

Look at it this way: just because something has not been directly observed to happen, does not mean it didn't/doesn't.

Perhaps not, but unless the claim cites a causally adequate process currently in operation and known to be capable of generating the claimed effects it is not a scientific claim, it is metaphysical. Are you making an appeal to the unknown?

I demand that you show me someone being raised from the dead by holiness/faith, or I won't believe it ever did. I demand that you show me Napoleon conquering even just 1 country, or I won't believe that he conquered several. Not only does your demand prove nothing, but also you will change it were an example given.

Demand what you like but I don’t make these claims. For someone who objects to logical fallacies you seem awfully fond of them.

So what we have at this point is the fact that the physical constants in this universe are fine-tuned and we know that mind is capable of fine-tuning while we are unaware of any natural process capable of fine-tuning. We also have coherent encoded digital information as fundamental and necessary component of biological systems and we know that mind is capable of generating encoded digital information while once again we are unaware of any natural process capable of generating this specific kind of information.

These are two pieces of evidence that suggests this universe and life in it was created. Furthermore since there is no causally adequate natural explanation for attributes of the universe or life in it, creation is currently the best explanation for both. This may change with new data but it is silly to deny the current reality.

First, you're changing the "information" goalposts. The original definition of "information" was in the genome, or in this case the configuration of components. Now you're saying that the kind of component also counts as information, and that the fitness function is information as well. The fitness function is a direct result of the environment, not the organism's genome. Make up your mind. What does "information" encompass?

Coherent Information trims away alternatives. When I say "It will rain", I have conveyed very little information but when I say "It will rain between 6 and 7 this morning in New Orleans" I have eliminated a great deal of alternative scenarios and have conveyed a great deal of information. In information theory the quantity of information is measured by the quantity of alternatives it eliminates. So when I said that the designer eliminated a huge number of alternative configurations that person inserted large amounts of information into the simulation.

Furthermore, it's naive to call a pile of gears and pendulums "functional parts." What is that supposed to mean? That a gear sitting in a lonely heap on a table is somehow "functional"? No, their "function" comes from their "genome", or rather the arrangement of parts inside the proto-clock. Merely supplying a gear does not help arrange these parts in any way.

I find your claim vacuous. Something is functional if it has a configuration that can be employed for any useful task. I am surprised you would deny this reality since these parts can and are used for multiple purposes with the same configuration. Likewise protein components have configurations that are functional and a great deal more that are disorganized blobs with no shape conformance, no stability and therefore no function because we know that protein components require shape stability, shape conformance and matched binding sites to be functional. Sequence conformance is generally not required.

The choice of gears and pendulums is arbitrarily. If my fitness function is "telling time," anything from a pile of sand to a stick stuck in the ground would suffice as starting places. Numerous different parts could be supplied to similar effects.

How can you demonstrate this to be true. I don't see any way for you to say they are arbitrary. If anything could have been used then the simulation would require these anythings to be included. They were not included because the simulation would have failed.

There are countless ways to make clocks, they are overlapping, codependent and no configuration is clearly "best." Your point?

 

There are countless ways to survive as a wild clock in the vast steppes of Timeberia.

I don't know if there are or not, but the designer of the simulator programmed it with a definition of best as opposed to "survive". Only those that run closest to the same speed as time survive. This is artificial, it is active information and it guarantees the simulation will suceed.

Do you actually believe this simulation demonstrates that natural processes are capable of generating the information required to generate functional systems?

It is interesting that you seem more interested in appeals to ridicule than in explaining your counter-claims.

Hmm, I reread my post and find it quite informative regarding the reasons the example is not relevant to this discussion. Was there something I said that requires elaboration?

There is minimal information imported into the simulation. It has building block -- gears, pendulums, springs, and so on -- and basic physics.

The designer only included functional parts. This amounts to an incredible amount of active information since the algorithm is guaranteed to apply only functional components. The designer also rigged an oracle to guarantee that correct fits are better than incorrect fits, more information.

Similarly, it could have had chemical "building blocks" and basic chemistry. A "target" is indeed in this case defined by a "designer", but that target could equally well have been "survive in the environment" and be defined by nature itself.

Survive in the wild is not a target as there are countless ways to survive in the wild, they are overlapping, codependent and no configuration is clearly "best".

At no point in the simulation did the "designer" help the parts achieve the "goal" of being clock-like. He did not nudge the parts and say "here, this'll work better to make a clock." He didn't even give the clocks an initial condition or setup.

No, importing information is a more subtle way to help out.

One can also observe numerous steps in the process from worthless clock to good clock. At no point did the "designer" give the system information on how to achieve any of these states. He did not "teach" it how to achieve proto-clock status or to develop a dial. This occurred through random mutation and selection.

Incorrect. The information added by the designer accomplished this task by eliminating innumerable unworkable combinations and the designer coded in an artificial fitness function that guaranteed success.

Are you defending this person's simulation because you actually believe it demonstrates that natural processes without aid and without importing any information (we can quibble about how much information was imported into this simulation but nobody can deny that some was imported and that information was critical to success of the simulation) can and does generate coherent information? If so can you provide a demonstration? If you don't believe this or you can't demonstrate it then why are we discussing this?

This is what is called a strawman, and also called moving the goalposts. I never claimed that a genetic algorithm has no information, so asking me to prove it does not is misleading. Also, I never claimed that you can make information without information, which is what you are now asking. Finally, the fact that an algorithm contains information does not in any way impair it from generating new information -- an arbitrarily large amount of information, to be exact.

First off unless I am mistaken, you quite clearly claimed that genetic algorithms only need the same attributes that evolution has to function. Perhaps you are claiming that evolutionary processes contain active information imported by a designer, but if not, then I have not mischaracterized your claim, I have not moved the goalpost, and you have claimed by induction that information can be made without information. Have I misunderstood your position?

Yet it is one step. Now it is a capability. What is to stop another step from being taken based on this new ability?

If it did take several more steps in fewer generations then it would be the example I was looking for. Speculation is nice but it is not evidence.

Genetic algorithms only need the same attributes as evolution has, to function. The most complicated would be the fitness function; but in evolution this comes naturally via death and reproduction. Likewise, you could implement a genetic algorithm with very little information, if you were to build every prototype yourself and input the outcome to the program; however, this would be absurdly time-consuming and expensive to do.

 

So because we design things to look like something natural, you conclude that the natural thing must be designed, is that it? I can make a rock, therefore rocks are designed?

Show me a genetic algorithm that does not import active information and I might agree with your claim. The reality is that they do not function without the designer artificially adding information to the search. In other words they function because the designer designed them to function. Likewise natural selection can only derive the diverse organisms we observe if there exists contiguous advantageous stepwise evolutionary pathways from one organism to another. I have asked for an example of a pathway just four steps long and I am certain that nobody will be able to provide even one. Yet if natural selection generated diversity then there would have to exist hundreds of millions of them each one of them hundreds of thousands long.

Actually I conclude that some things are natural because natural processes in operation today are observed to generate them. It is because life has the appearance of and contents that we observe only design processes construct and never natural processes that I conclude that design is a possible explanation for life. I personally believe there may be other processes yet to be discovered so I have not "concluded" that life was designed, however I note that currently design is the better explanation since there is no coherent natural explanation at this time that is causally adequate in that it cites known processes in operation today that have been shown to be capable of generating the effects ascribed to it.

What design? Who designed evolution, or what makes evolution not be a genetic algorithm?

Genetic algorithms are all designed and purposely import active information. Are you sure you want to place evolution into that category?

My prior commitment is a Young Earth Creationist, a position which I was forced after decades of kicking and struggling, to abandon. Look in the archives of this forum if you do not believe me, and you will see that for yourself. It is your prior commitments which drag you down, not mine.

I am speaking of your prior commitment (and certainty) to natural processes that have not been shown capable of generating the effects you have assigned to them. I know of no other prior commitments you hold and they don't seem relevant to this discussion. What prior commitment have you noticed I subscribe to because I don't think I have offered any.

Oh, no no no no. This ability did not already exist; it was newly created during the experiment. The ability to use citrate may have existed elsewhere, but not in the sample in the experiment (not under oxidizing conditions). Just like if aliens 1 trillion light-years from here invented a lightbulb, doesn't mean that we didn't invent it too.

Sure I don't see that I implied that the experiment previously contained the derived mutations, but the mutations were an alteration of a pre-existing capability to metabolize citrate in deoxygenated conditions. This is clearly an adaptation. Furthermore the mutations involved fewer than four steps and was well within the reach of a blind random search.

 

The first minute or two don't entirely apply here; it's the simulation I wanted to point at. The simulation of numerous random mutations occurring to bring about functional improvements to a device, in only a few thousand generations.

 

(Actually, I'd love to get the code of this simulator running for fun, and perhaps work on improving it...)

I don't find the slide show or the code particularly informative to this subject. The simulation quite obviously imports substantial information and also has a target defined by the designer. It is interesting in that it illustrates the narrative regarding selection very well but it does not in any way demonstrate that natural selection is actually capable of generating what it purports to generate. A better description of it is documentary/propaganda.