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Comment Re:not evolution (Score 1) 387

So you can bring those to bear on the subject of finches and cliff swallows? Please, do cite away.

No, I bring those to bear on the larger issue of evolution.

So if a population oscillates between two dominant phenotypes (small beak/big beak; short wings/long wings), you are satisfied that this is an example of evolution even if there are no net changes to the organism's genome?

If that trait is being passed on to offspring, then yes, it is. In the case of Darwin's finches, you have distinct species(little to no interbreeding) which inhabit different niches and which display morphological differences which are readily apparent. You can find similar examples in ring species. The cliff swallows are indeed evolution(provided that the traits are indeed being passed on to offspring), but this is not a speciation event(at least, not yet).

And you find that this is strong evidence that over a time period of millions/billions of years, that this oscillation will result in an entirely different animal?

Since this is couched within the larger body of evidence regarding evolution, certainly. As for what type of animal the decendents of those birds will be, it all depends on the variety of environmental pressures which are exerted upon the species. In a few million years, those swallows may well give rise to flightless sea birds. In a few million years, invasive species in the Galapagos Islands may lead to the evolution of larger meat eating finches. Genetic drift may lead to something entirely unexpected. And they may all just go extinct, leaving some other species to adapt and fill their respective niches. It would take the ability to see the future to know how environmental pressures are going to affect their genomes in next few million years.

If there is no net change over hundreds of years, how do you that into non-zero net change over millions of years?

I said drastic evolutionary change. Those species are indeed ungoing evolution right now. Every species is. The process runs on geological time. We can chart genetic change, but you have already made it clear that you hold to the creationist idea of there being different "types" of evolution. You won't be satisfied by anything short of a major morphological change happening in your lifetime. Do you also dismiss plate tectonics because mountains don't spring up over the course of a human lifetime?

We can both accuse each other of obfuscation, but I haven't relied on accusations of dishonesty and ignorance.

Good for you. Having cornered many creationists into finally admitting their a priori assumptions, I no longer have the patience to assume that someone who is presenting the same old arguments is doing so in good faith.

I don't find it useful to slap "evolution" on any type of change, when the character of the change is entirely different.

The character is not different. That's the point.

Does a child "evolve" into an adult?

Is a child a population?

Comment Re:not evolution (Score 1) 387

When was that observed? Oh, it wasn't? You're extrapolating based on fossil evidence? That's nice.

Fossil evidence, DNA evidence, geological evidence. You know, converging lines of evidence.

You still aren't talking about the finches. Did you concede that as a point?

Nope. Why would I? You have simply rehashed an old creationist canard which is usually presented to assert that microeveolution occurs while macroevolution does not. It's also usually presented as an example of Biblical "kinds." It is certainly an example of evolution. Whether it is an example of complete speciation is another question, but it has no bearing on the larger issue.

If you're going to concede the finches, which of those other "numerous" examples are based on observation of live specimens, and which are extrapolations from fossil records?

We have exactly two categories of specimens to examine: live and dead. The expectation that we are going to see vast evolutionary leaps in real time is part of this distorted view of evolution that you are pushing. It doesn't correspond to reality or to the theory of evolution. You can choose to ignore evidence from fossils and DNA comparisons all you like. It's just dishonest.

Do you think it is useful for the sake of scientific observation to distinguish between "evolution" that results in no change, as opposed to "evolution" that results in brand new organisms?

All evolution, by definition, results in change. So, no, it's not a useful distinction. It's just an attempt to evade the obvious conclusions of evolutionary theory.

s it impossible to distinguish between the two, even though Darwin's finches are still finches after hundreds of years of "evolving"?

I'm tempted to rescind my prior apology. Are you really so obtuse that you think that we should expect some drastic evolutionary change in those finches in hundreds of years?

Do you prefer a scientific lexicon that deliberately obfuscates different activity by using the same word in different senses?

No, I prefer honesty in approaching science and evidence, not deliberate obfuscation to support creationism.

Comment Re:not evolution (Score 1) 387

"All the time" ... Observed how?

Examples include trisomy, insertions and gene duplication.

In short, no, human mutation rate was not measured. They compared human and chimp genomes, assumed the difference is due to evolution and then treated that difference as the human mutation rate using dates derived from evolutionary assumptions. Exactly what you just said before in summary, which I challenged for being circular when used as a rebuttal to my challenge.

Point taken. So, start here, then(a good overview of precisely the mistake I made). The lowest estimated mutation rate based simply upon human genomes is 1.0 x 10-8 per site per generation. Still the same order of magnitude, so it won't have a substantial effect on my point.

Read this and question for a moment the fallibility of human imagination.

And I suggest you read some of the comments by actual paleotologists on that page.

Then look at these two pictures and tell me why the concept art is "scientific" as opposed to "fantasy"

Because we also have fossils of the related species as well, which gives us a good idea of how the intermediate species will look. But, then, judging by your later comments, you've already decided that physiology can't be derived from fossil records, so I wouldn't expect it to matter.

See, if evolution is true, then there's no reason why we can't one day reverse engineer DNA completely (hey, it's random and we're semi-intelligent). At that point in time, we can create any arbitrary DNA sequence, and should be able to reconstruct the intermediate life forms from the DNA sequences. If it happened once by lucky circumstances, we can do it again, intentionally.

And why would you assume that? We could create a lookalike, but we will never know if we got all of the genes correct.

In short, there's nothing in natural selection that can select against specific base pair mutations. Natural selection can't select for the future, it only compares against now.

Of course.

Not by natural selection based on overall fitness, but by highly specific genetic "error-check" systems (against what reference?).

What are you talking about? I am talking about death. An organism with a broken metabolism won't survive past a single cell stage. An organism lacking cellular adhesion would not survive past that stage. No "reference" involved at all. Things that are broken just die.

Now how did natural selection work *before* that system evolved into existence, and where is your evidence that life works without it? (Even "basic" bacteria have this functionality)

Early life would have had more errors in transcription, which is exactly what we would expect. Later, as gene expression became more robust and complicated, selection pressure would increase for less error prone mechanisms.

It was a starting point to illustrate the enormity of the problem

And, as I pointed out, you ignored the reality of the theory in order to artificially inflate the problem.

This is part of why I don't consider evolutionary theory to be "solid scientific fact" as you do - it fails to do rigorous mathematical modeling. If it is so plausible, there should be math that puts my rough model to shame; and yet I haven't seen anything that attempts to capture the probabilities involved or how evolution comfortably meets the challenge.

That is because you are starting off from a bad theoretical foundation and expecting the theory to match up to that.

Take away the "evolution by natural selection" examples, and all you have left is a bunch of pseudo-history extrapolated from tea-leaves-esque fossil readings.

"Take away some of the proof, and all you have left is evidence that I personally disagree with."

Comment Re:not evolution (Score 1) 387

You ignored the grandparent's discussion of Australopithecus in favor of focusing on finches. Let's look at the parts of their questions that you cut out:

Right. What is the alternative, add up a lot of small changes and then not see any change? Australopithecus came down from the trees, got longer legs, shorter arms, better vision, upright posture, wider pelvis, smaller teeth and a larger brain. Is it still an Australopithecus, or is it now a Homo Habilis? I fail to see any logic in your statement, these small changes have added up to a new animal.

Why did you ignore this? Is it because it doesn't fit your "all changes are minimal," sine wave theory? Australopithecus is not just a variation of humans. We don't vacillate between those extremes. Why are you ignoring the thousands of examples out there of biological change over time in favor of your static vision of species?

This is why I bandied the term "ignorant" around. Either you are not aware of the numerous examples of cumulative changes resulting in new species, or you are. One is a form of ignorance, which is blameless and can be easily remedied. The other is a rejection of the evidence, and, given the fact that you are a literate human with access to the Internet for research, is far more problematic. I apologize for being dismissive, but I am really trying to get you to justify your position that changes over time cannot add up to speciation events.

Comment Re:not evolution (Score 1) 387

Is natural selection an algorithm that is "looking for" humans?

Nope. We are just a happy accident in the history of life.

That inheritance improves the odds slightly was not in question. The point was that there are other unaccounted forces (survival, environmental changes, luck) working against the unaccounted filtering effect, such that you cannot assume progress just because a filtering effect exists.

Given that the evidence supports the fact that this is in fact what happened, that assumption is more than justified.

Do you believe that 3.1 Gbs of human genome is filler? If true, you should be able to irradiate and randomly mutate somewhere around 99% of a human's DNA sequence with no ill effect.

See, this is where your simplified version gets you into trouble. Genes are added to genomes all the time, from gene copying mistakes to interspecies breeding to bacterial gene interchange to endogenous retroviruses. Entire chromosomes are sometimes duplicated. Random events are adding genetic material all the time, and natural selection is winnowing out the non-working combinations.

You assumed that humans evolved from chimpanzees, extrapolated that rate to the past, and found it reasonable that humans evolved from chimpanzees and fish. That's circular reasoning.

Nope. I demonstrated that, if evolutionary theory is true, the rate of change as demonstrated by our closest living relatives is consistent with the amount of time that change had to have happened, which is precisely what you are denying.

Can you support the assumed human mutation rate with a measured human mutation rate?

Sure. Start here:

The average mutation rate was estimated to be ~2.5 × 108 mutations per nucleotide site or 175 mutations per diploid genome per generation

6 million years divided by an average generation time(20 years for humans, 15 for chimpanzees, so 17.5 average for both species) gives us 342,857 generations. This yields 59,999,975 mutations.

Can we reverse engineer all those intermediate organisms? (Can't do that now, but should be possible if evolution is true!)

Can we extrapolate the likely form and location of the intermediate organisms? Sure. That's how we discovered Tiktaalik, for example. The researchers worked from an understanding of the development of the tetrapods and the population distribution in the fossil records and predicted that they would find a proto-tetrapod in Devonian strata in Canada. And they did. As for whether they can be recreated exactly, then no, and there is no reason to expect it to be possible at all. We can compare related organisms to determine which genes were likely conserved or developed independently. That can get us in the ballpark(which is why we can infer a lot about intermediate species), but recreating an entire extinct genome is likely never going to be possible.

Filters always remove information. At best, with an analog signal carrying digital encoded information, you can remove the noise without harming the information.

Hey, you are almost there! Congrats!

Filters can be a part of an overall creative process

Bingo! That's what I was saying!

A random string generator has the potential to "write" a novel.

Indeed. And I have generated the first paragraph of "Romeo & Julliette" using one that starts with a small string of random gibberish and uses random mutations and selection to generate it. Of course, the couplet is just a model used to represent a theoretical genome which is fit to survive in a particular environment.

Having solved that simpler problem, does natural selection really behave like the filter you built?

Natural selection works on a higher level, so to speak. Genes live or die in the organisms which they build. So, while the filters represent a high level view of how natural selection works, it would take a few more steps to make it more realistic: interpreting the "genome," building an "organism" from that genome and allowing it to compete in a simulated environment. This is, coincidentally, one of my current personal projects.

Every organism has a sequence: be born, mature, survive, reproduce. That is a meaning that natural selection has to find, even though it doesn't know how to look for it.

OK, let's go with that, noting that we are ignoring a large part of the organisms on earth. Most catastrophic genetic combinations are selecting against before birth. If an organism has a problem with low level protein synthesis, it probably won't make it through gestation. This process continues throughout the organism's lifetime. If they can't compete for resources, they are less likely to live long enough to pass on their genes. If they can't escape predation, they are less likely to live long enough to pass on their genes. If they can't compete in mating, they are less likely to live long enough to pass on their genes. And so on. Natural selection isn't "looking" for something. There is no "correct" genome which is the goal. There is no goal. There is no intelligence. There is just life, death and adaptation.

Yes, I get that you're saying it. The math you have offered is insufficient to support it though. Using simplified models that assume things in your favor is not how you "proof of concept" the numbers.

Funny, coming from someone who started with a ludicrous "tornado in a junkyard" style argument to pick apart a straw man representation of evolutionary theory.

"It works in theory" does not mean "it works in practice".

You have it backwards. We saw that it worked in practice, and constructed a theory to fit the evidence.

On the flip side, I can "disproof of concept" with a model that assumes in your favor; if you can't do it in favorable conditions, you obviously can't do it in disfavorable conditions.

No, your model disproves a model of evolution which exists only in your head.

All barbs aside, I would say that you should seriously consider taking some courses in population biology and evolutionary biology.

Comment Re:not evolution (Score 1) 387

Faced with an inability to defend your assertion, you have switched topics. Keep digging.

You are the one switching topics. The fossil record clearly demonstrates the changes in lifeforms over billions of years. You refute that by appealing to a sine wave, with no justification for ignoring the evidence. Saying that you are ignorant is the kindest assumption.

Comment Re:not evolution (Score 1) 387

Your model is incapable of failure (extinction), which makes it rigged.

And your model ignores everything we know about the development of life, which makes it at best an example of a complete misunderstanding of evolution.

It assumes that every single "correct" base pair you hit is "hard-saved" from ever being lost. Your model only takes 25-30 independent rolls to "hit" the target, because every dice is rolled in parallel and is utterly independent of the dice around it.

And you completely miss the point. My example is a very crude example of how filters turn random input into non-random output. Of course it doesn't take into account mutations, extinctions, etc. It's a model which can be expressed in a short Perl script, after all. But it's still closer to what is actually happening than the mess you posted.

Certainly there's no real world guarantee that every "correct" mutation to the genome gets saved and never gets corrupted.

Of course not. That's a legacy of my model. And I've made more complex models which do not guaranteee survival of "correct" genes and model sexual reproduction, random deletions, random additions and various mutations. The same filtering process is apparent there, too.

(Natural selection is going to determine survival or death with 100% certainty based on a single base pair mutation in a 10 million/1 billion base pair sequence?)

If the mutation is sufficiently detrimental, certainly. Most of the time, it is not. You and I both have novel mutations in our genes which are not present in our parents. Yet, we've survived long enough to type out these messages, and I've survived long enough to reproduce, so my novel combinations have a chance to perpetuate.

The models we've used also ignore that code doesn't work incrementally. Half of a protein is more likely going to be a non-effective protein rather than a half-effective protein. The dice are interdependent. "THE" is a word and has meaning. "TNE" is not.

Proteins do not have to be perfectly effective to work. And non-functional or semi-functional proteins are not necessarily detrimental to survival, thus having no effect on survivability. For example, suppose a primitive proto-bacteria had a duplication event and now two proto-genes are generating the same protein. This very well may have no effect on its ability to reproduce(and it very well could, too; there are no guarantees). However, now one of those copies can be subject to mutation without affecting the original protein. It may end up non-functional(so called "junk DNA"), it may end mutating and functioning slightly different from the original gene(like the many related proteins responsible for blood clotting) or it may end up deleted at some point. In fact, if you want a good example of how proteins can evolve, look up the evolutionary history of blood clotting mechanisms.

So let's try a different analysis. How many generations do you need to get from "nothing" to human? If we assume each generation can add one "correct" base pair, that takes 3 billion generations.

Given that we share a large part of our genes with bacteria, roughly along the lines of 40%, then a lot of that took place rather rapidly. At a generation rate of 20 minutes and shooting for 40%(1.2 billion generations), that takes 937,000 years, roughly. Subtract that from 3.6 billion years, and you have a 40% human genome with 3.599 billion years left to generate the remaining 60%. The generations do get longer for multicellular organisms, but that is counter balanced by the development of sexual reproduction which speeds up the exchange of novel and complimentary genetic changes.

Let's look at it from the opposite side. We differ from chimpanzees by roughly 2% of our DNA, or 60 million base pairs. We diverged from their line about 6 million years ago. That's a rate of 10 base pair changes per year. Using that rate, we have a possible 5 billion base changes in the past 500 million years, which is roughly the age of fish. We only differ from fish by about 25% of our DNA, or 750 million base pairs. At that rate, there was enough time to evolve a human from a fish 6.6 times.

Of course, in reality, generation times and mutation rates vary, as does the environment. The point here is that your numbers don't reflect reality. You apply math to a straw man version of evolution.

If natural selection only removes individuals from the population, it cannot increase genetic diversity, which means it cannot add the information needed to get from life Zero to humanity.

I fail to see what you are missing here. Natural selection doesn't generate new genetic material. Sure. It acts as a filter on genetic material, new or otherwise, and that's what turns the random introduction of genetical material and reconfigurations into non-random genetic diversity. Call it additive, call it creative, call it destructive, whatever. The semantics don't change the function.

Perfect natural selection does improve your chances if it only lets the "most correct" individuals reproduce, but that assumes a winner take all system where every tiny reproductive advantage is propagated across the entire population in a short period of time. That's not how large populations work.

"Perfect natural selection" is not required. Nor is it a part of actual evolutionary biology.

I don't believe in guided evolution. I'm saying you need to believe it if you want the numbers to work.

And I'm saying you are dead wrong.

Comment Re:not evolution (Score 1) 387

Well, you have demonstrated that you have no clue how evolution actually works, so congratulations on that. I would suggest some remedial high school biology. You haven't even made it to Behe's level.

I'll use a more basic example for you. Suppose that we had 65 six sided dice, and that 65 sixes represents a particular complex genome(you could use any combination of 65 results, but it is mathematically immaterial). Randomly hitting that result has a probability of 3.8x10^50. That would correspond to the silly conception that you are using above. Pretty damned unlikely. But, then, that bears no resemblance to actual evolutionary theory. Take a very much simplified version where results of 6 are kept. At that point, it generally only takes 25-30 rolls to get the required result. Quite a difference, wouldn't you say? Here's a simple example of that in Perl if you want to try it yourself:

#!/usr/bin/perl

my $number_of_sixes = 0;
my $number_of_rolls = 0;
my $number_of_attempts = 1000;
my $total_rolls = 0;

for(my $i = 0; $i while($number_of_sixes my $number_of_dice = 65 - $number_of_sixes;

while($number_of_dice > 0) {
my $dice_roll = int(rand(6)) + 1;
if ($dice_roll == 6) {
$number_of_sixes++;
}
$number_of_dice--;
}
$number_of_rolls++;
}
$total_rolls += $number_of_rolls;
}
print "Total number of rolls: $total_rolls\n";
print "Total number of experiments: $number_of_attempts\n";
print "Average number of rolls to get 6 dice each time: " . $total_rolls/$number_of_attempts . "\n";

Now, in reality, natural selection acts as a filter on the random inputs of genetic additions. Thus, your prime mistake is exemplified in this statement:

you still need to try 1.8e1e8 possibilities before you might randomly hit the human combination

Natural selection acts to conserve working combinations and discard detrimental combinations. Just like applying the filter of selecting 6's dramtically drops the required number of tries to reach an unlikely outcome, so to does natural selection radically drop the generations required to reach complex lifeforms.

You just agreed with me that natural selection does not generate new genetic material. It is incapable of creating, is it only able to destroy the failures.

Non sequitur. It does not follow that because natural selection does not generate new genetic material that it is a process which is only destructive. It facilitates increased fitness. This is certainly an additive or, as you seem to prefer, creative process.

Random mutation doesn't have enough tries in several billion years to exhaust the entire sample space of "possible genetic combinations".

Since such a thing isn't remotely required by evolution, this is another non sequitur.

That leaves non-random mutation, which is "guided" mutation - but then we need a mechanism that provides non-random mutation, which as I note is "unexplained" and "unobserved".

No, this is just your attempt to interject a "god of the gaps" into your inability(or refusal) to correctly understand what evolutionary theory is and how it works. A sadly common occurance.

Comment Re:not evolution (Score 1) 387

You do not have enough time for random mutations to generate enough possible answers for natural selection to sift out the "right ones".

3.6 billion years is plenty of time.

You're left with some unexplained and unobserved form of guided mutation, which natural selection is incapable of providing.

What a useless, unsupported claim. Who was guiding this "guided mutation" that you start with? And upon what grounds are you basing your idea that natural selection is incapable of producing the results we see?

Comment Re:Useless hindsight (Score 1) 387

So tell me, how does knowing the theory of evolution change any of your decisions today, tomorrow or any time in the future? In my book, if it does not make a prediction that can be proven, then it's useless.

I'm not the parent, but I'll answer. As I pointed out before, it is quite useful for prediction. But, it certainly does have an effect on my decisions. The use of antibiotics, for example, is a decision which is affected by the fact that bacteria evolve quickly. My choice of diet and activity is affected by what I know of the evolutionary history of my species. My choice of pets is partially dictated by evolution(I avoid certain breeds of cats and dogs due to genetic problems). And, of course, if you count indirect effects, evolution touches on virtually everything I experience, from social interactions to my appreciation of nature.

Finally, I would study evolution for no reason other than to learn. I am not one to revel in ignorance and call it pragmatism.

Comment Re:Useless hindsight (Score 1) 387

So Darwin made a proposition, not a prediction.

He made predictions, too. For example, a famous moth that, in 1862, he predicted must exist was finally discovered in 1903.

But that's not all. Let's try a more recent example. Based on evolutionary theory, several paleotologists began searching Ellesmere Island in Canada for examples of proto-tetrapods in sediment from the Devonian period. And guess what they found, just where they had predicted? This little bugger.

Evolutionary theory is actually very useful in predicting things, from the probable location of certain fossils to the genetic changes which occurred in the various families that results in the species we see today. Go look at whale evolution and how it was worked out, for another example.

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