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Thursday, February 07, 2019

Maximal mutations

As I promised last night, here are the numbers I utilized in last night's debate on the theory of evolution by natural selection with biologist JF Gariepy:

BACTERIA
Years: 3,800,000,000
Years per generation: 0.000071347 (37.5 mins per generation)
Generations per fixed mutation: 1600
Years per fixed mutation: 0.114
Maximum fixed mutations: 33,288,000,916

Source: Sequencing of 19 whole genomes detected 25 mutations that were fixed in the 40,000 generations of the experiment.
NATURE, 2009

NOTE: These 25 mutations were fixed in parallel. The 1600 generations per fixed mutation represent an average. So, JF's appeal to massive parallel propagation is already accounted for, at least with regards to observed fixation in bacteria.


MAMMALS
Years: 200,000,000
Years per generation: 4.3
Generations per fixed mutation: 1600
Years per fixed mutation: 6880
Maximum fixed mutations: 29,070

NOTE: the bottom number represents the maximum number of fixed mutations from Morganucodontid to Homo sapiens sapiens.


CHLCA
Years: 9,000,000
Years per generation: 20
Generations per fixed mutation: 1600
Years per fixed mutation: 32000
Maximum fixed mutations: 125

NOTE: the 9 million represents the latest average estimate for the Chimpanzee-Human Last Common Ancestor, which estimate has ranged from as little as 4 million years on the basis of the molecular clock to 25 million years.

Now, the primary problem with JF's appeal to parallel gene propagation is that it requires a minimum of 15,000,000 mutations to become fixed in the human population, and another 15,000,000 mutations to become fixed in the chimpanzee population, and to do so in an amount of time that permits 125 fixed mutations in series.

In other words, there must be 120,000 genes simultaneously fixing throughout the entire population in parallel at all times, and the same process has to happen TWICE. This does not strike me as credible, even if we don't bother questioning JF's claim that the observed genetic differences between human and chimpanzee lie on a spectrum and that not all humans will possess the 15 million mutations that separate Homo sapiens sapiens from Pan troglodytes and that not all chimpanzees possess the additional 15 million mutations that separate Pan troglodytes from Homo sapiens sapiens.

Or, to put it more simply, there have been 450,000 chimp and human generations since the CHLCA. Based on the number of mutations observed fixing in parallel in the Nature study, that would permit 562 total fixed mutations in that time frame. Which is only 29,999,438 short of the approximate number observed.

I understand that some people are disappointed that I did not drive these points home during the debate, or that I did not answer JF's rhetoric with any rhetorical killshots of my own. But JF is not, and has never been, my target. I'm hunting much bigger game. That being said, I will analyze his program and make use of it at some point in the not-too-distant future.

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224 Comments:

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Blogger FUBARwest February 07, 2019 8:59 AM  

Will you be discussing this with JF again? He ended it prematurely right around the time you were about to drive home a point.

Blogger S1AL February 07, 2019 9:01 AM  

"[N]ot all humans will possess the 15 million mutations that separate Homo sapiens sapiens from Pan troglodytes and that not all chimpanzees possess the additional 15 million mutations that separate Pan troglodytes from Homo sapiens sapiens."

One of these mentions of pan troglodytes is supposed to be something else?

Blogger Fozzy Bear February 07, 2019 9:04 AM  

I thought it was strange, that after VD started with the observed rate of mutations, JF claimed the observed rate needed to be multiplied millions of times to fit TENS theory.

Blogger FUBARwest February 07, 2019 9:09 AM  

"I thought it was strange, that after VD started with the observed rate of mutations, JF claimed the observed rate needed to be multiplied millions of times to fit TENS theory."

I thought it was strange that whenever JFG saw a potential attack vector that Vox was going to utilize he attacked it in the most superficial way possible to dismiss it often times not realizing it hurt his case. "Not all humans have the same eyes."

You would think a "scientist", a moral nihilist at that, would be 100% on board with exploding new territory and new ideas. Especially ones that go against the orthodoxy of the time.

Blogger PragmaticTroll February 07, 2019 9:10 AM  

Stay dialectic, Ponyboy. Stay dialectic.

Blogger VD February 07, 2019 9:19 AM  

Will you be discussing this with JF again?

Not anytime soon. I will want to incorporate massive parallel fixation into the model first.

Blogger VD February 07, 2019 9:20 AM  

One of these mentions of pan troglodytes is supposed to be something else?

No. The actual division of the 30 million estimated mutational differences is likely not 50/50, but it serves to demonstrate the point.

Blogger maniacprovost February 07, 2019 9:20 AM  

You need to normalize based on the population size in the experiment versus historical population size.

I don't know the best way to get mutation rate for humans, but I would imagine it is lower than for bacteria. Bacteria are single celled and have different methods of reprpduction and gene transfer.

Blogger David Ray Milton February 07, 2019 9:30 AM  

I’m looking forward to hearing more. It was a good discussion between you two, but only after sleep and reflection did I realize how weak his argument was based on your math. The thing is, I think JF must know of the weakness is in the argument. He kept trying to sweep your argument away by saying, “Eh Vox Day, deez mutations are appening every wir simultaneously wit every individual.”

Okay, right. But that’s not the problem. The problem is how do those mutations that occur in individuals become fixed across the entire gene pool even if you view that gene pool on a broad spectrum unless every mutation is perfectly heritable? And in my understanding of genetics, no traits are perfectly heritable.

I’m new at contemplating all of this, but it seems like a massive hole in TENS.

Blogger Gregory the Great February 07, 2019 9:31 AM  

In the Jay Dyer debate JF repeated said "I'm a monkey". If we accept this as truth the number of mutations required for the CHLCA transition obviously is zero in his case.

Blogger Rocklea Marina February 07, 2019 9:32 AM  

I thought the most telling part of JF's defence was at 39 minutes when he claimed that species are not real categories. I get he was trying to say fixed point categories will vary over time, but that is the entire point of trying to find the rate of fixed mutations. Is TENS really to be viewed as just the mutations of three categories, the "everlasting fingerprint", when the phenotype is packaged in convenient bags of blood and bone so that we can get a reasonable estimate of the number of generations and categorize the different expressions?

Blogger Nate February 07, 2019 9:43 AM  

jesus. the discrepancy is bigger than we imagined.

Anonymous Anonymous February 07, 2019 9:44 AM  

A lot of these discussions resemble the things people say when they’re talking about economics only in terms of promised benefits of a purchase without looking at the costs and doing a cost/benefit analysis. It’s a child’s way to look at the world.

When you focus only on the required fixing time and selection of positive mutations, while ignoring the negative mutations, you’re doing the same thing but 10,000 times worse.

Because the negative mutations have to be selected OUT or they will eradicate the species long before it has time to evolve into anything else. This means the selection cost has to be consistent and consistently high, of the order of 90%.

The odds of any positive mutations not being paired with a number of negative mutations are massively against any positive mutations surviving more than a few generations.

All that’s assuming you accept that “positive” mutations, in the sense of conveying reproductive advantages sufficient to become ubiquitous, even exist. This has yet to be demonstrated.

None of the above even touches on the information problems so manfully ignored by advocates of TENS.

Blogger Passionate Observer February 07, 2019 9:47 AM  

Proving that the divergence between humans and other primates can not be explained by mutation alone does not disprove evolution, because the theory of evolution does not require the human species to originate via that specific mechanism.

The best way to make this case would be to look at the expected mutations between several different primate species with common ancestors, not just humans and chimps, and see how many pairs of species show unexpected results.

If it turns out that comparisons between all non-human primates show the expected mutation rate but comparisons involving humans and other primates are anomalous, then what you've done is strengthened the human origin via hybridization hypothesis rather than attacking the theory of evolution.

Blogger Gregory the Great February 07, 2019 9:55 AM  

It is strange that so many people will say they cannot believe in God, but they find it easy to believe in an infinite multiverse with infinite parallel words.

Blogger S1AL February 07, 2019 10:00 AM  

"No. The actual division of the 30 million estimated mutational differences is likely not 50/50, but it serves to demonstrate the point."

I mean that you compared HSS to PT twice in the same sentence... Unless I'm missing something from above, one of those comparisons should be chimpanzees?

Blogger FUBARwest February 07, 2019 10:04 AM  

One requires submitting the other doesnt. I'd respect them more if they came out and said it.

Blogger Станислав Бартошевич February 07, 2019 10:16 AM  

@13
Because the negative mutations have to be selected OUT or they will eradicate the species long before it has time to evolve into anything else. This means the selection cost has to be consistent and consistently high, of the order of 90%.

It gets worse than that. Given any rate of mutation that does not drive the time required for evolution well beyond the accepted age of the Universe, higher animals simply would be unable to bear the selection cost, given that from each pair of parents at least 2 descendants (actually a good deal more, given deaths to random factors for which fitness of a particular organism is irrelevant) offspring must be left to maintain the species.

And then there is the problem of the vast majority of mutations, both theoretical beneficial mutations and quite evident deleterious ones (did that study that measured fixed mutations in bacteria bothered to check if any of those mutations did the bacteria any good?) being nearly neutral, and thus invisible to any sort of natural selection.

Blogger Slagenthor February 07, 2019 10:20 AM  

Bigger game indeed. Genetics will be the death of TENS. This is before the origin of information question and the execution machinery.

Hat tip to Vox.

Blogger Rory February 07, 2019 10:21 AM  

I missed the debate, and not sure if I'll have time to go back and watch it. Does anyone mind ELI5'ing what the argument is here please? It sounds like it's essentially "The number of fixed mutations in the human genome can't have happened in the time it took for humans to evolve", but I'm not really following what's being said above (biology / evolution isn't something I know a lot about).

Blogger Jeff Burton February 07, 2019 10:28 AM  

Haldane's Dilemna. But Wikipedia tells me Kimura solved this with "neutral evolution": while we have mutations fixing under selective pressure (and the population paying the requisite substitutional costs), there are other wonderful mutations bubbling just just below the visibility of natural selection, spreading throughout the population, and poised to pop up as selective advantages when the time is ripe, pre-fixed and ready to go. Right.

BTW, the human mutation rate is about 100 per individual, mostly running from very bad to only a little bit bad. Which is a whole 'nother problem for TENS. Because does a species shed those at the same time it's trying to fix the very, very few beneficial ones?

Blogger 1st Earl Hardwicke February 07, 2019 10:28 AM  

This comment has been removed by the author.

Blogger 1st Earl Hardwicke February 07, 2019 10:32 AM  

This comment has been removed by the author.

Blogger Rick February 07, 2019 10:32 AM  

“But JF is not, and has never been, my target. I'm hunting much bigger game.”

Excellent news!

Blogger Count Nomis February 07, 2019 10:35 AM  

Both JF and Vox are totally out of date in both your arguments. The field of evolution has passed you by. Suggest you read When Evolution Stops.

Blogger 1st Earl Hardwicke February 07, 2019 10:35 AM  

So does maximal exclude mutations that may occur in caves as the result of Radon gas?

Blogger Rick February 07, 2019 10:37 AM  

VD — did you have a gut instinct, before you did any math, that the TENS time frame just isn’t long enough?

Blogger The Deuce February 07, 2019 10:45 AM  

Also worth pointing out: Accounting for a fast enough rate of fixed mutations is only the BEGINNING of the conceptual problems that need to be accounted for, because fixed genetic changes by themselves don't explain anything. It's quite possible to have large-scale genetic change with basically no phenotypic change and no new structures or biological functions. Ultimately what we're trying to explain in biology, and what Darwinism is meant to account for, is the existence of *biological function*, which the underlying genetics are necessary but not sufficient to account for.

It's not JUST mutation fixation in general that must be accounted for, which is compatible with both large-scale functional changes and no functional changes and therefore explains neither, but specifically how mutations fixed in a way that added up to the large-scale functional differences between humans and chimps specifically.

Also, you could insert human DNA into a chimp zygote and stick it into a chimp mother and all you'd end up with is a dead cell. So even the specific genes aren't enough to explain the difference. You need a human phenotype cell and mother to "interpret" the human DNA. So the genetic changes have to have happened such that the interpreters evolved together with the genes being interpreted in order to interpret it correctly.

And finally, you get into the thorniest problem of all, which is the philosophy of mind issue. The biggest and most obvious change in biological function that needs to be accounted for is the human capacity for abstract thought, specifically our ability to engage in logical reasoning, which has led to buildings and airplanes and Youtube debates about evolution. When we reason, we grasp the logical relationships between propositions, and we use our grasp of those relationships to follow premises to rational conclusions.

The logical relationships between propositions are universal. If a logical argument is correct, then it is correct for you and me and everyone. It would be correct even if nobody existed, and it is correct in any other universes that may exist. A logical argument for evolution, say, cannot be true for JF and false for Vox, and to say otherwise is to abandon all science and reason completely.

But all material objects and states of affairs (like, say, genes) are contingent rather than universal, and pass into and out of existence. Each individual is made out of different material from every other individual. No two people share the same genes. The genes of identical twins may share identical *patterns* (but patterns themselves aren't material objects), but the the actual strands of DNA are of course distinct physical objects, and in fact are distinct between each cell in the body of a single person.

So by definition, no material object has the characteristic of applying universally to all people and all possible universes that the logical relationships between propositions do.

So any attempt to explain the function of human reasoning in material terms (including genetics) implies that the universal logical relationships between propositions actually plays no role in it, which implies that we don't really grasp the relationships between propositions and we don't really follow premises to conclusions, and that there is therefore no such thing as rational argument (for evolution or anything else) and truth it utterly relative and subjective, Jordan Peterson style.

So to bring it all back to the beginning, the failure to even account for a fast enough mutation fixation rate, while ignoring all the other constraints those mutations must have, is just the first and least serious failure in a whole cascade of conceptual failure.

Blogger birdman February 07, 2019 11:03 AM  

Need a better take than that

Blogger The Deuce February 07, 2019 11:06 AM  

Jeff Burton wrote:Haldane's Dilemna. But Wikipedia tells me Kimura solved this with "neutral evolution": while we have mutations fixing under selective pressure (and the population paying the requisite substitutional costs), there are other wonderful mutations bubbling just just below the visibility of natural selection, spreading throughout the population, and poised to pop up as selective advantages when the time is ripe, pre-fixed and ready to go.

The problem with neutral mutations is, it's an appeal to raw chance. The whole point of natural selection was to explain the appearance of sophisticated biological function by appealing to a pseudo-designer, because raw random chance was no explanation at all. Appealing to the possibility of a bunch of neutral mutations spontaneously coming together to create some new biological function that they were not previously selected for is no more explanatory than just appealing to a super-lucky bunch of mutations happening at once to do the same thing.

Blogger birdman February 07, 2019 11:09 AM  

But a lot of people still believing that shits as a fact without even questioning it or skeptic about it

Blogger FUBARwest February 07, 2019 11:15 AM  

"Both JF and Vox are totally out of date in both your arguments. The field of evolution has passed you by. Suggest you read When Evolution Stops."

Second or third time you've said this. Say what you think is so relevant.

Blogger Xiety February 07, 2019 11:28 AM  

S1AL: 15m fixed mutations in the direction CHLCA -> human, 15m fixed mutations in the direction CHLCA -> chimp. Parallel separations of human from chimp, and chimp from human.

Blogger Azure Amaranthine February 07, 2019 11:31 AM  

"But JF is not, and has never been, my target. I'm hunting much bigger game."

This is why everyone who matters loves professional big game hunters.

"I don't know the best way to get mutation rate for humans, but I would imagine it is lower than for bacteria."

I would assume it's in the ballpark per generation, but obviously bacteria have much faster generations. Bacteria do have the advantage of potential horizontal gene transfer though, so a beneficial mutation might be expected to be more easily and rapidly fixed.

"Because the negative mutations have to be selected OUT or they will eradicate the species long before it has time to evolve into anything else. This means the selection cost has to be consistent and consistently high, of the order of 90%."

Someone was saying that it was around 90% for humans. I wouldn't expect it to be the same for everything. If this is true, I would expect TENS adherents to be some of the biggest voices calling for women to stay in the home and the kitchen, since they'd need 20 children per woman on average just for us to avoid degeneration. After that, THEN they'd have the mass weeding-out of persons with detrimental mutations... either by murder or sterilization.

"If it turns out that comparisons between all non-human primates show the expected mutation rate but comparisons involving humans and other primates are anomalous, then what you've done is strengthened the human origin via hybridization hypothesis rather than attacking the theory of evolution."

Such hybrids would as far as I can tell HAVE to be artificial in nature. That being said, yes it is attacking TENS. Evolution is no longer your creator... aliens are. And that's the most probabilistically charitable interpretation of "hybrids".

"It gets worse than that. Given any rate of mutation that does not drive the time required for evolution well beyond the accepted age of the Universe, higher animals simply would be unable to bear the selection cost"

And there's the other rock and a hard place scenario. "What if selection pressures/mutation rates were increased by some currently unobserved punctuated process?" A: All higher life subject to that enough to potentially drive these rates would now be dead.

"This is before the origin of information question and the execution machinery."

True, but this thrust is more about kicking goo-to-you proponents and honorary chimps in the nuts. Not that the execution/interpretation point isn't fully capable of doing that for those whom can wrap their heads around it, but more tools to force retreat into delusion bubbles is nearly always better.

"BTW, the human mutation rate is about 100 per individual, mostly running from very bad to only a little bit bad."

If that's true, humanity is a very tall and frail genetic giant indeed. Even Madam Fortuna doesn't like those odds. The bigger they are, the harder they fall. We'd be far and away unable to even sustain our present "evolutionary advantages" with our current modes of reproduction.

As for the neutral mutation argument, it's just a restatement of punctuated equilibrium. The same absurdity repackaged conceptually to look different while having exactly the same obvious flaws.

Blogger Passionate Observer February 07, 2019 11:41 AM  

Azure Amaranthine wrote:Such hybrids would as far as I can tell HAVE to be artificial in nature.

Do you believe the platapus was created by aliens? Now that we've sequenced its genome we know what always was intuitively obvious: its ancestors were mammal-bird hybrids.

This is a more distant cross than any proposed primate - non-primate mammal hybridization proposed as the basis of human origin.

Blogger CO February 07, 2019 11:57 AM  

"And then there is the problem of the vast majority of mutations, both theoretical beneficial mutations and quite evident deleterious ones (did that study that measured fixed mutations in bacteria bothered to check if any of those mutations did the bacteria any good?) being nearly neutral, and thus invisible to any sort of natural selection. "

No need. It's all good (the mutations that is) /s

Mutations are like providence just trust it all work itself out ;-)

Blogger Passionate Observer February 07, 2019 11:59 AM  

Rory wrote:Does anyone mind ELI5'ing what the argument is here please?
People who are opposed to evolution on a theological basis have one last holdout for a secular justification for their skepticism: whether or not the mechanism of random mutation is sufficient to explain the observed changes in the genome.

The relatively recent discoveries of at least half a dozen additional mechanisms for creating genetic changes hasn't sunk in with them yet, so they're proceed as if proving the insufficiency of random mutation represents a new accomplishment rather than a known fact.

The only real source of confusion is that on both sides of the argument, incorporation of new data tends to be limited to the generational changeover rate of the people involved. Many biologists are also not up speed on the newest discoveries, and so will instinctively try to defend obsolete positions.

Blogger FUBARwest February 07, 2019 12:04 PM  

"The relatively recent discoveries of at least half a dozen additional mechanisms for creating genetic changes hasn't sunk in with them yet,"

What are these recent discoveries and how do they change the rate of mutation and the timeline we are presented with?

Blogger Latro Cottidianus February 07, 2019 12:05 PM  

I'm curious as a non-expert how population bottlenecks might change the rate of fixation. Doubtful it can be helpful to either side as you can't use a bottleneck to explain away every single instance of speciation but I'd imagine wiping out 90% of a population at random could lead to faster fixation by chance of who survives.

Blogger Silly but True February 07, 2019 12:08 PM  

So essentially Metropolis may be correct: and the pan-troglodytes still can win / are winning / will win?

Blogger Reno Chris February 07, 2019 12:14 PM  

Even what you present is mostly hand waving as bad as it appears. If you take into account the fossil record which states what actually happened the picture is much worse. Mammals are given 200 million years, but for the first 140 million years, very little change happened and there were only a few different mammal species, all small and rodent like. beginning about 60 million years ago at the KT boundary (also the point of the big dinosaur die off), mammals explode and in something less than 10 million years go from a hand full of species to the thousands that we know. small rodents suddenly become whales, elephants, cats, apes and all the others that we find. This is the great mammal radiation or explosion.

Blogger Azure Amaranthine February 07, 2019 12:21 PM  

"This is a more distant cross than any proposed primate - non-primate mammal hybridization proposed as the basis of human origin."

You realize that that's physically impossible without artificial assistance, right? Heck, we can't even mate with "other" primates. Speculating that at some point we magically mated with something even more genetically distant.... yeaaaaaah no.

I anticipated this, which is why I pointed out that alien interference was the charitable interpretation.

"Now that we've sequenced its genome we know what always was intuitively obvious: its ancestors were mammal-bird hybrids."

"He went in assumptions blazing, then came out with his ass in his hands and a mortal head wound. We needed a brain transplant, and well, they're both mostly fat in his case, so...."

That's not how reproduction works.

"People who are opposed to evolution on a theological basis have one last holdout for a secular justification for their skepticism"

Chip off the old block, just like his father. Or in other words, liar sighted.

Blogger Sam February 07, 2019 12:21 PM  

@34
"I would assume it's in the ballpark per generation, but obviously bacteria have much faster generations. Bacteria do have the advantage of potential horizontal gene transfer though, so a beneficial mutation might be expected to be more easily and rapidly fixed."

It depends on species. Correcting mutations has a resource cost and you can have higher and lower rates of mutation; species that are adapted to high levels of radiation for example have really good DNA repair mechanisms for instance.

"Someone was saying that it was around 90% for humans. I wouldn't expect it to be the same for everything. If this is true, I would expect TENS adherents to be some of the biggest voices calling for women to stay in the home and the kitchen, since they'd need 20 children per woman on average just for us to avoid degeneration. After that, THEN they'd have the mass weeding-out of persons with detrimental mutations... either by murder or sterilization."

The eugenics movement did have parts that synced up with that; however the sane parts of eugenics are 'racist' so it died in the 1960s.

"Such hybrids would as far as I can tell HAVE to be artificial in nature. That being said, yes it is attacking TENS. Evolution is no longer your creator... aliens are. And that's the most probabilistically charitable interpretation of "hybrids"."

I believe they are talking about stuff like mating with Neanderthals.

Blogger Jeff Burton February 07, 2019 12:24 PM  

"at least half a dozen additional mechanisms for creating genetic changes"
This argument only starts with mechanisms for genetic change. It's also about how those changes spread through populations.

Re population bottlenecks - google "Error Catastrophe".

Blogger Passionate Observer February 07, 2019 12:27 PM  

@42 This is what I was talking about when I said that debates like this move at the speed of human generational changeover rather than the speed of data acquisition.

The next generation of evolutionary biologists and creationists are both going to have better arguments on this subject, because they will have grown up incorporating the data which has accrued since your personal cutoff date for accepting new facts.

I won't bother telling you that every statement you made about hybridization is trivially disprovable, because if you were interested in that sort of thing you would have verified your claims before making them.

Blogger David Ray Milton February 07, 2019 12:29 PM  

Dismissing opposition to TENS by claiming theological bias against it is odd as Vox openly mentioned in the debate that he is not a young earth creationist nor does he favor any particular explanation for life’s origin.

And I really love the “you giez are reaaallly out of date on your research” posts that keep coming in.

One of the main critiques against TENS that has been repeatedly brought up is that theory is modified every 5 to 10 years in order to make it palatable to new data. That’s a problem.

Blogger VD February 07, 2019 12:29 PM  

Both JF and Vox are totally out of date in both your arguments. The field of evolution has passed you by.

Always nice to hear from the Gammas. I'm sure we're all impressed by what a Smart Boy you are.

I'd imagine wiping out 90% of a population at random could lead to faster fixation by chance of who survives.

Actually, it doesn't work that way. It has been observed that the smaller the population, the more likely it is that beneficial mutations are lost.

Blogger Azure Amaranthine February 07, 2019 12:41 PM  

"This is what I was talking about when I said that debates like this move at the speed of human generational changeover rather than the speed of data acquisition."

"Science advances one obituary at a time."

"The next generation of evolutionary biologists and creationists are both going to have better arguments on this subject, because they will have grown up incorporating the data which has accrued since your personal cutoff date for accepting new facts."

Until the combined education and organizational limit.

"I won't bother telling you that every statement you made about hybridization is trivially disprovable"

Right, so, crossbreed two different classes of animals, such as Mammalia and Aves. If you want a serious argument it needs to be relatively high life forms, vertebrates or more specific, because that's what you're claiming on both of your counts. Else, show where someone else has done it or observed it in recorded human history.

I'm open to new information, but stuff you pulled out of your ass based on what your personal philosophy required does not satisfy that requisite.

Prediction: The closest you'll come is an argument along the lines of "by hybridization I mean they didn't speciate the same way X did", which is a regress to a form of "speciation doesn't matter". Unfortunately for you, setting the metrics and then claiming they don't exist when they contradict you does not a convincing argument make. Again, that is the most charitable interpretation of what you are claiming.

Blogger Latro Cottidianus February 07, 2019 12:43 PM  

*Actually, it doesn't work that way. It has been observed that the smaller the population, the more likely it is that beneficial mutations are lost.*

That's true, I meant more that in some small fraction of circumstances you could end up with that 10% being primarily an emergent mutation. But of course you can't rely upon that to explain the innumerable differences between species.

Though Vox if you are interested in incorporating JF's parallel fixation into your argument and need to analyze a more put together version of the theory I did come across a paper that attempted to provide a mathematical model. I haven't had the time to go over it myself and you may have already seen it in your research:
https://www.pnas.org/content/107/52/22454.full

Blogger Jeff Burton February 07, 2019 12:52 PM  

@Passionate Observer
These multiple new sources of genetic change. Please educate me. And please put the ones that are not stochastic in all caps.

Blogger Passionate Observer February 07, 2019 12:55 PM  

Azure Amaranthine wrote:I'm open to new information, but stuff you pulled out of your ass based on what your personal philosophy required does not satisfy that requisite.
Your claim to be open to new information would be more credible if you were capable of refraining from libel.

Nevertheless, if you want to examine the arguments yourself you could go directly to the source:

http://www.macroevolution.net/human-origins.html

...or review summaries of the debate:

(2013) https://phys.org/news/2013-07-human-hybrids-closer-theory-evidence.html
(2017) https://theoutline.com/post/1547/did-we-come-from-pigs

Blogger Snidely Whiplash February 07, 2019 1:02 PM  

Passionate Observer wrote:Do you believe the platapus was created by aliens? Now that we've sequenced its genome we know what always was intuitively obvious: its ancestors were mammal-bird hybrids.
Not they weren't. I can state this unequivocally.
There is simply no natural mechanism by which this can come about, even the idea that some absurd freak event could create a single individual does not cover the need for a breeding population.
The genetic overlap with birds is easily understood if you accept evolution. You need to remember that both birds and mammals are held to be descended from dinosaurs. The branch between monotremes and livebearing mammals would just have to be much further back than the split between placental mammals and marsupials, before the appearance of the X chromosome and the disappearance of the egg shell.

Blogger Unknown February 07, 2019 1:02 PM  

A consequence of parallel mutation that was immediately apparent to me was ingroup exclusion and outgrouo inclusion. Outgrouo inclusion, the ability for members of different species to breed with each other is actually not uncommon. Here is a link to Wikipedia list of such cases.

https://en.m.wikipedia.org/wiki/List_of_genetic_hybrids

The ingroup exclusion, the inability of populations of the same species breeding with each other, should also be relatively common. Example is some breeds of dogs cannot breed with each other.

The question is how much of these two phenomenons should we expect to see based on parallel mutation?

Blogger Snidely Whiplash February 07, 2019 1:07 PM  

Passionate Observer wrote:I won't bother telling you that every statement you made about hybridization is trivially disprovable, because if you were interested in that sort of thing you would have verified your claims before making them.
HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA

So would you, buddy.

Blogger maniacprovost February 07, 2019 1:10 PM  

Actually, it doesn't work that way. It has been observed that the smaller the population, the more likely it is that beneficial mutations are lost.

I am interested to research this statement. What's interesting though is that humans instinctively segregate into smaller breeding pools based on racial proximity. This slows down the transfer of genes but also concentrates recessives.

Evolutionary mechanisms are subject to evolution, which adds a whole layer of complexity requirement.

Blogger Passionate Observer February 07, 2019 1:16 PM  

You, an internet expert:

Snidely Whiplash wrote:There is simply no natural mechanism by which this can come about, even the idea that some absurd freak event could create a single individual does not cover the need for a breeding population.

Some moronic geneticist who wasted a three decade career studying hybridization:

"Moreover, in mammalian hybrid crosses, the male hybrids are usually more sterile than are the females. In a commercial context, this fact means that livestock breeders typically backcross F₁ hybrids of the fertile sex back to one parent or the other. They do not, as a rule, produce new breeds by breeding the first cross hybrids among themselves. Often, even after a backcross, only the females are fertile among the resulting hybrids. So repeated backcrossing is typical. Commonly there are two or more generations of backcrossing before fertile hybrids of both sexes are obtained and the new breed can be maintained via matings among the hybrids themselves. More backcrossing tends to be necessary in cases where the parents participating in the original cross are more distantly related."

Blogger One Deplorable DT February 07, 2019 1:18 PM  

Passionate Observer - you've been asked twice to list the 'new sources of genetic change.' Once @38 by FUBARwest who also asked how they change the rate of mutation and the timeline. And again @50 by Jeff Burton.

You can now add a third request.

Rules of the blog are that you answer direct, relevant questions, and not just with a link. (A link in addition to an answer is welcome.) So let's see the list. Preferably without the attitude you've displayed towards other commenters so far.

@51 - https://theoutline.com/post/1547/did-we-come-from-pigs

Let's see..."one scientist"...who "does not have genetic evidence to support his hypothesis"...believes humans are the result of a chimpanzee and a pig having sex and producing viable offspring because...body fat...female orgasms...and a few other things.

And the example given to show this may be possible is a coyote and a domesticated dog having sex and producing viable offspring. Head smack.

You know...I'll skip the temptation to ridicule it. Chimpanzees and pigs exist today which means his hypothesis can be quickly and easily tested.

* Can he get a chimpanzee and a pig to mate?
* Absent that, can he artificially inseminate one by the other?
* In either case, are viable offspring produced? And do they in any way represent a move towards humanity, i.e. the human genome?

Absent a successful test this isn't worth discussing since Eugene McCarthy can't hide behind "...millions of years..." to avoid direct, repeatable testing.

https://phys.org/news/2013-07-human-hybrids-closer-theory-evidence.html

Ah...the same theory from four years earlier. So in 4 years he never attempted a test? Or did I miss that from skimming? Eager to know the results and if this represents a radical new source of genetic change.*

* That still couldn't overcome Shannon entropy to explain how the source DNA came to exist in the first place, but we'll ignore that for the moment.

Blogger L' Aristokrato February 07, 2019 1:18 PM  

This debate needs to be continued; preferably at a time when JF doesn't sound like he's dying of the cancer-AIDS. You and him having a bit more info on each others' positions might help in making a sequel more interesting.

Blogger Silent Draco February 07, 2019 1:25 PM  

Several more things affect mutation rate on the genes. The three-codon groups of nucleotides give 64 combinations, for 21 amino acids and for control language. Some of the codes are for start, stop, skip transcription. A number of genes contain duplicate or backup sections. A mutation of T for C nucleotide on DNA may not make a change, if there's an unchanged copy on the gene to use. A mutation affecting one of the control codes can create disaster and nonviable embryos. This goes for both sets of DNA in a cell: nuclear and mitochondrial.

Something that's harder to grasp is that the DNA transcripts to messenger RNA, then transcripts to transcription RNA, which provide the structures for building proteins in a cell. This works fine inside one cell, but what in turn drives groups of cells to become defined and delineated tissues, such as organs, glands, bones, and brain? That's the mechanism set which drives speciation, and it must also be coded into the genes somehow.

Blogger Unknown February 07, 2019 1:30 PM  

Reading the article linked at the top of the post, I see that it goes on to compare the significance of the bacterial measurements to the mutation rate in humans.

Notably, the rate they determine is per base pair, not per genome. The human genome is approximately 3 orders of magnitude larger than the bacterial genome, so that adds 3 orders of magnitude to the rate.

Second they note the difference between 'per replication' and 'per generation'. Going from gamete to gamete in humans takes many replications, and their estimate is that it is on the rough order of 100 replications per generation.

Thus, the mutation rate in humans is approximately 5 orders of magnitude higher per generation than it is for bacteria. That gets us from your 125 mutations to... 12.5 million. That's awfully close to your 15 million target, suggesting the timeframes are about right.

Did I miss a step in the calculation?

Blogger Unknown February 07, 2019 1:30 PM  

This comment has been removed by the author.

Blogger Passionate Observer February 07, 2019 1:33 PM  

@57 I also asked for the mutation rate analysis between chimps and humans to be repeated, but for two non-human primates but I don't see anyone jumping on that request, so I'm not inclined to jump through hoops for anyone else.

Chimp-human specialization allegedly can not be explained by observed mutation rates. All well and good, but is this observation valid only for chimps and humans, or is it a general issue with most other species as well?

If most species show normal rates of mutation based on time since divergence, but humans are not, then that's simply evidence of human speciation occurring via a different mechanism.

Blogger Trebor Nosemaj February 07, 2019 1:33 PM  

I'm having trouble keeping up. I'm up to the 5 times multiplication table. You keep going on Vox, I'll catch up.

Anonymous Anonymous February 07, 2019 1:40 PM  

"I won't bother telling you that every statement you made about hybridization is trivially disprovable, because if you were interested in that sort of thing you would have verified your claims before making them."

Convenient, I admit.

Not really how it works, though. If they really were trivially disprovable you'd have disproved them instead of mouthing off about it.

Your choice of response indicates your actual belief far more clearly than your claim.

Blogger SirHamster February 07, 2019 1:40 PM  

FUBARwest wrote:"Both JF and Vox are totally out of date in both your arguments. The field of evolution has passed you by. Suggest you read When Evolution Stops."

Second or third time you've said this. Say what you think is so relevant.


If he did that instead of name-dropping, he'd sound even more retarded.

From the book's excerpt:
"At its basis, the present theory postulates that it is extraterrestrial impacts, with the occasionally resulting volcanism, that is the generating power for speciation."

TLDR: Meteors and volcanoes did it.

You catch that, Vox? Your overlooking these generous hints from Secret King has undermined all of your efforts!

Blogger David Fenger February 07, 2019 1:41 PM  

Expanding on my earlier 5 orders of magnitude comment (@60), I see I forgot to link my source - I searched for the source of the Nature 2009 article, and came up with this article discussing the study:

http://book.bionumbers.org/what-is-the-mutation-rate-during-genome-replication/

Apologies for the 'Unknown' and double-comment, I haven't commented here in ages.

Blogger Aidan MacLear February 07, 2019 1:46 PM  

This might be above my mathematical pay grade, so correct me if I'm wrong here, but what about population bottlenecks? It wouldn't help with the rate of mutation, but it would help explain how certain genes become ubiquitous throughout the human population.

The bacteria in the study that discovered the rate of mutation were not subject to selection pressures, therefore it is unnaturally unlikely that any of them become fixed in the population. If a mutation provides an organism with a reproductive advantage over its peers, it can become fixed in a population within a single generation.

For example, a single hominid smart enough to manufacture spears could arm his kin or tribe, kill the males of every other tribe in the geographical vicinity, and establish his genetics as a significant proportion of his species' genome within a single lifetime; the Genghis Khan effect. And his sons are well positioned to do the same and spread the mutation even farther.

Anonymous Anonymous February 07, 2019 1:49 PM  

"Moreover, in mammalian hybrid crosses ... "

Bait and switch.

I feel a dishonesty banning coming on.

Blogger The Deuce February 07, 2019 1:57 PM  

Good lord, the gamma posturing is strong with Passionate Observer.

Secret king internet expert dismisses all those biologists who aren't on the cutting edge as he is:

"Many biologists are also not up speed on the newest discoveries, and so will instinctively try to defend obsolete positions."

About an hour later:

"You, an internet expert: ... Some moronic geneticist who wasted a three decade career studying hybridization:"


Btw, we've been assured that there are "dozens" of proven new mechanisms for introducing genetic changes into populations besides random mutation (even though, logically, any genetic change that gets introduced to a member of a population and wasn't previously selected for the effect it has in that population is functionally identical to a random mutation). And yet so far, the only one he's mentioned has turned out to be an extremely dubious hypothesis about platypuses being the result of a mammal mating with a bird.

Blogger One Deplorable DT February 07, 2019 1:58 PM  

@62 - I also asked for the mutation rate analysis between chimps and humans to be repeated, but for two non-human primates but I don't see anyone jumping on that request, so I'm not inclined to jump through hoops for anyone else.

You did not ask someone for this. You threw it out as a general suggestion, presumably as a line for Vox and JF to pursue in their debate.

If you want to pose the question directly I imagine you would have to pose it to Vox since it's related to his claims. Though since he is the owner of the blog he has the luxury of ignoring the rules. Or deferring until he's ready to present his complete case.

You, on the other hand, have claimed that there are 'new sources of genetic change' that commentators here know nothing about. And you've used that claim to dismiss points made by others without any further explanation. You've been directly asked three times to list these new sources which you presume no one here is familiar with. It shouldn't be difficult to list each one with a simple, one sentence explanation. So...let's have the list. Please. We're all eager to learn (if there is something to learn).

Anonymous Anonymous February 07, 2019 2:01 PM  

David Fenger

In your comment at @60, were you quoting the mutation rate or the rate of fixed mutations?

Blogger SirHamster February 07, 2019 2:01 PM  

Vox's pink polar bear experiment may not be as far fetched as originally thought.

Pink squirrels observed.

Blogger David Fenger February 07, 2019 2:08 PM  

@71 The article discusses both. The rate of fixation for the bacteria was measured (and matches the numbers above). The rest went on to discuss rates of mutation.

Early on the article worked back from the study to a mutation rate that would cause the number of fixations seen (10^-10 mutations per bp per replication), but didn't show the math, and I'm not personally familiar with how to convert mutation rate to fixation rate.

It stands to reason, however, that fixation rate is proportional to mutation rate. I'll grant I haven't backed that up with math, I'd have to do some digging on the subject.

Blogger Passionate Observer February 07, 2019 2:10 PM  

One Deplorable DT wrote:We're all eager to learn (if there is something to learn).
Long story short, I don't believe you. I did believe Sammi Hass in last night's thread, which is why he received a different response.

Blogger Tom February 07, 2019 2:12 PM  

The difference between JF and VD's positions and methods are the same differences that existed between Aristotle and Bacon. JF's position is not unique among evolutionists.

JF uses Aristotelian deductive reasoning, going from the General to the Specific, while VD is using Baconian (founder of scientific method), Inductive reasoning, going from the specific to the general.

JF's theory is deductive in nature, and seeks explanations to rationalize his deductive conclusions. Much like alchemists of old attributed much of how materials react to mysticism.

Robert Boyle was a Baconian. He believed that amassing data by experiment would allow him to discover new laws of Nature. And he was right. Using the inductive method he tore away the alchemists’ bonds of mysticism, unleashing chemistry as a genuine quantitative science.

The scientific method, A.K.A. Hypothetico-deductive method, is a procedure for the construction of a scientific theory that will account for results obtained through direct observation and experimentation and that will, through inference, predict further effects that can then be verified or disproved by empirical evidence derived from other experiments or observations.

JF, works from the general "we see a wide variety of life forms", and works backwards based on assumptions to deduce that life evolved. Logically JF's position is rational, but when applied to reality fails. The observed specifics don't result in the general conclusion.

JF's hypothesis, is not written in such a way that clear criteria are stated to establish its falseness. If his hypothesis were verifiable or falsifiable, then in the 400 years since Bacon created what is now called the Scientific Method, we would have seen clear observable evidence of the evolution complex multi cellular animals, not just variants of natural selection such as yeast becoming some other form of yeast.

Alternatively if his hypothesis were verifiable, accurate predictions of future new complex multi cellular organisms or at least new organs/systems could be created and verified. JF's novel approach to evolution cannot and does not create accurate predictions, and using his "program" to calculate mutation rates in parallel, as VD has done, falsifies his hypothesis, so his hypothesis must change to meet reality, or be discarded as false.

Blogger One Deplorable DT February 07, 2019 2:16 PM  

@74 - Long story short, I don't believe you. I did believe Sammi Hass in last night's thread, which is why he received a different response.

Long story short: it doesn't matter what you believe. Please follow the rules of the blog. List the new sources of genetic change which you believe no one here is familiar with.

To save you time, you don't even need to provide links. A list with enough of a description that we can all Google is fine. Clearly you have something in mind otherwise you wouldn't be making the claim. Let's see it.

Blogger Snidely Whiplash February 07, 2019 2:16 PM  

Passionate Observer wrote:Some moronic geneticist who wasted a three decade career studying hybridization:
Find me a hybrid that crosses the genus line, let alone family, let alone class. Every known hybrid involving vertebrates is within the genus, and more often is between subspecies within the species. One of the more distant hybrids is the mule, a hybrid of the horse and the ass (your role models, I suppose). Mules (horse x ass) present as male and are never fertile. Hinnies (ass x horse) present as female and one in ten thousand is fertile. If such an animal is born (there have been a few hundred over all the years of mule breeding), and manages to breed, the occurrence is rare enough that the introduced genes will be eliminated within a few generations, unless they provide some massive advantage. This is why, even though horses and asses overlap in parts of their natural ranges, there is not any gene transference detectable between the populations.
The idea that some freak mating between an early mammal and a bird, which is rightly assumed to be impossible, can be repeated in the next generation is simply absurd.
You have literally no idea what you're talking about.

Spend a few years breeding livestock then come back here and tell us all about this amazing theory you read on a website. It may not cure you of your idiocy, but it may teach you keep your mouth shut when you're an ignorant pustule.

Blogger FUBARwest February 07, 2019 2:22 PM  

"Long story short, I don't believe you. I did believe Sammi Hass in last night's thread, which is why he received a different response."

I still haven't gotten a response yet. You don't believe me either? What did I ever do to you?

Anonymous Anonymous February 07, 2019 2:31 PM  

You asked a question. As Fred Reed could tell you, asking questions is denying science.

@73

David Fenger;

I agree there must be some relationship between them. I have no idea what it is but I expect the ratio to be ... quite large. I was curious if the numbers you were presenting indicated that this gap had been crossed or was yet ahead.

Thanks.

Blogger Francis Parker Yockey February 07, 2019 2:35 PM  

But Wikipedia tells me Kimura solved this with "neutral evolution": while we have mutations fixing under selective pressure (and the population paying the requisite substitutional costs), there are other wonderful mutations bubbling just just below the visibility of natural selection, spreading throughout the population, and poised to pop up as selective advantages when the time is ripe, pre-fixed and ready to go. Right.

Example: high levels of endemic infectious disease select for, not just particular HLA types, but greater HLA variability.

Blogger Sammi Hass February 07, 2019 2:37 PM  

Oof. Please leave me out of it, Observer.

Blogger Azure Amaranthine February 07, 2019 2:38 PM  

"Your claim to be open to new information would be more credible if you were capable of refraining from libel."

Ahh, so it was someone else's ass, and you sucked it right up because you failed biology in high school.

"http://www.macroevolution.net/human-origins.html"

HELL YES! I was waiting for one of you pigpanzee freaks to appear!

His evidences by my observation:
>95% wild and domestic animals, animals that very only in coat patterns or slight superficial characteristics, or animals that vary in usual territory
<6% Photographs and hearsay of supposed freaks with a complete absence of genetic evidence, cow-dog, horse-dog, cat-dog, cow-moose, horse-camel, elephant-horse, the list goes on and the rule remains, zero genetic evidence, maybe one to two usually vague photos if lucky, miscellaneous hearsay.

"Some moronic geneticist who wasted a three decade career studying hybridization

And conveniently has precisely zero genetic evidence for any hybridization more disparate than the above.

Geneticist who doesn't have genetic evidence says what again? Look, I know it sucks to be a dupe, but if you can't own up you'll be a dupe forever.

"Outgrouo inclusion, the ability for members of different species to breed with each other is actually not uncommon."

Yes it is uncommon. Not unknown does not equal common. Results tend heavily toward failure to implant, followed by failure to be born alive, followed by failure to survive to adulthood, followed by failure to be fertile, followed by decreasing degrees of infertility, in order of likelihood and genetic distance.

Blogger Francis Parker Yockey February 07, 2019 2:45 PM  

CTRL-F " gene " = 8 hits

CTRL-F " allele " = zero hits.

Hmmm...

Blogger Snidely Whiplash February 07, 2019 2:51 PM  

Francis Parker Yockey wrote:Hmmm...
Stop with the posturing you pointless moron.

Blogger David Fenger February 07, 2019 2:53 PM  

@79 Of course the ratio is large. But all it needs to be is linear, so that doubling the mutation rate doubles the fixation rate. A quick peek at the Wikipedia article on Fixation (population genetics) confirms that the rates are proportional.

So if the rate of mutations for humans is 100,000 times higher per generation than it is for bacteria, then the rate of fixation should be 100,000 times higher. 125 calculated using the bacteria fixation rate becomes 12,500,000 for humans.

Blogger Ryan G February 07, 2019 3:07 PM  

This comment has been removed by the author.

Blogger Ryan G February 07, 2019 3:11 PM  

One of the problems with debating evolution is that the whole thing is based upon a tautology: there is no refuting it by virtue of how the theory is structured.

Species are always mutating, always changing to become more adapted to their environment. Except for all the species that are unchanged since the time of the dinosaurs (or before).

Mutation is a blind tinkerer, never building towards anything. Except for the times when 'neutral' mutations just so happen to accumulate, somehow, in spite of neither helping or hindering the organism, until they result in a positive mutation.

Natural selection is a mindless, mechanistic process which simply confers reproductive advantages to those individuals best suited for their environment. Except for all the times when species 'need' something - like longer necks, the ability to swim deeper, or relocate organs or orifices.

There's no way you can refute evolution without first getting evolutionists to accept some kind of objective metric by which it can be invalidated. The only things I've heard of are somewhat facetious remarks about "finding a rabbit in the cretaceous" or other things which still assume evolution to be true before it can be proven false.

I appreciate the work Vox is doing, and I personally find it convincing, but evolutionists always have an "out". Even if his points were to be widely accepted, I suspect they'll just come up with another bit of plausible sounding speculation to hand wave it away.

Blogger Blastman February 07, 2019 3:29 PM  

It's a good observation that evolutionists own published mutation rates don’t' even support evolution.

But as The Deuce pointed out, the mutation rate is irrelevant if mutations can't accomplish what it needs to explain all the various structures and biochemical functions observed in the various forms of life.

Not By Chance -- Dr. Lee Spenter … (p 159, 160, 131)

Mutations for those steps have never been observed. …

The neo-Darwinians would like us to believe that large evolutionary changes can result from a series of small events if there are enough of them. But if these events all lose information they can’t be the steps in the kind of evolution NDT is supposed to explain, no matter how many mutations there are.

… among all the mutations that have been studied, there aren’t any known, clear, examples of a mutation that has added information. Of course, I cannot, nor can anyone else, demonstrate the negative thesis that there are no such mutations at all. Surely, I don’t know all examples of mutations. There are examples out there that nobody has yet discovered. But so far is known, or at least so far as I know, there are no such examples.

Not even one mutation has been observed that adds a little information to the genome. That surely shows there are not the millions upon millions of potential mutations the theory demands.


What is the ratio of good to deleterious mutations? 1-100? 1 - 1000? Going downhill, not uphill. There are trivial examples where a species can adapt through environmental pressure (natural selection), but this is extremely limited in scope and doesn't amount to evolution.

The essential problem for evolution -- what mechanism is there to build up new genetic material with new genetic functions? In other words, how do you get from a bacterium like E. Coli with 4,800 genes, to a worm with 19,000 genes? You need at a minimum 14,200 new genes representing millions and millions of new base pairs. In addition there are 1000's of new structures and coordinated intricate biochemical processes that are needed too. Mutations are not even close to explaining these.

Blogger Passionate Observer February 07, 2019 3:30 PM  

Sammi Hass wrote:Please leave me out of it
It's tragic, but not surprising, that this blog is a place where you're unable to accept complements for honorable behavior without exposing yourself to danger.

Blogger Blastman February 07, 2019 3:32 PM  

Passionate Observer

The relatively recent discoveries of at least half a dozen additional mechanisms for creating genetic changes hasn't sunk in with them yet, so they're proceed as if proving the insufficiency of random mutation represents a new accomplishment rather than a known fact.


That's old news.

There are many mechanisms of change in organisms. In fact, one of the biologists who frequents the discussions over at UD (Uncommon Descent), has a home page with over 50 listed mechanisms of change. The problem is, none of these mechanisms builds up new and novel genetic functions. Here is a biology professor who teaches at a major university in the US -- who has been challenged at UD to provide examples of the build up of new genetic features -- and he can't do it. Again, that is the essential problem for evolution. There's change that can happen in organisms, but it is not the type of changes that are required to demonstrate evolution. There is no scientific observed evidence of the building up of new and novel genetic functions and features going on.

Things like lateral gene transfers do not address the problem of building up new, novel, genetic functions. Lateral transfers are just the mixing and matching of already existing genetic material. How did that genetic material arise in the first place so it could then be moved around?

We don’t see even so much as a paper clip self-assemble through the material forces of nature -- chemistry + physics + chance. Yet, we are suppose to believe that these natural forces, which is all evolution has to work with, can create a human heart, lungs, liver, kidneys, eyes and all the organs of the body, … and … the 1000’s of biochemical processes that go along with these organs that work in intricate co-ordination. Just a bolt of lightening here or there into some pond or swamp, and that will do the trick to get things started? The more we know and study about biochemistry and the intricacies of life the more ridiculous the evolutionist claims look.

What amazes me about the people that buy into the evolution paradigm, is that they actually have to believe that just the material forces of nature -- chemistry + physics + chance -- are capable of building complex machines on their own. We can build 747’s and send people to the moon in rockets but we can’t even assemble the simplest of life in a laboratory. Yet … poof … it just somehow happened, and we're working on that, but in the meantime just trust us on evolution?

Blogger Azure Amaranthine February 07, 2019 3:34 PM  

"exposing yourself to danger"

Words on a blog where you're semi-anonymous are so dangerous, apparently. Ridicule hurts? What soft beings we are become.

Blogger FUBARwest February 07, 2019 3:36 PM  

"It's tragic, but not surprising, that this blog is a place where you're unable to accept complements for honorable behavior without exposing yourself to danger."

Am I ever going to get an answer to my question?

Anonymous Anonymous February 07, 2019 3:38 PM  

This is not a safe space, true.

But it is civil and it has rules.

In this thread, you are the one person to have broken them.

So, who should Sammi be concerned about?

Blogger One Deplorable DT February 07, 2019 3:47 PM  

@92 - Am I ever going to get an answer to my question?

No, but if you press him on it you might get a few more excuses.

@88 @90 Blastman - Vox has chosen to focus on and attack observable mutation rates, and I'm very interested to see how this ends up.

But I'm in agreement with you regarding mutation and truly new genetic information even if evolutionists had the rates they dream of.

Blogger Azure Amaranthine February 07, 2019 3:48 PM  

"So if the rate of mutations for humans is 100,000 times higher per generation than it is for bacteria, then the rate of fixation should be 100,000 times higher. 125 calculated using the bacteria fixation rate becomes 12,500,000 for humans."

Look, I can tell you immediately without even writing it down that that cannot possibly be true.

"rates are proportional"

No. There's your first error. It's not proportional to mutation. It's proportional to population size, inversely. Your second error is that the ratio is to average generational duration, not directly to time.

Blogger Snidely Whiplash February 07, 2019 3:48 PM  

Passionate Observer wrote:It's tragic, but not surprising, that this blog is a place where you're unable to accept complements for honorable behavior without exposing yourself to danger.
She's not afraid, fuckwit. She's embarrassed to be seen in your comments. She wants nothing whatever to do with you. Are you really this deaf to normal human language?

Sneering is not a good look even on people who are superior. In your case it's just pathetic.

Blogger Sammi Hass February 07, 2019 3:51 PM  

I'm not in danger at all here. I come from a 1000-year-plus line of elite Kings Guards. I am the danger you warn me about. You were asked to follow blog rules several times by several regulars. You must know by now that I live and breathe honor and duty and I have none to you. Do not use me as your shield, Passionate Observer. Viking women were known to be more ruthless than the men and I am certainly no exception.

Blogger Silly but True February 07, 2019 3:54 PM  

Platypuses are amazing.

Males are poisonous with 83 toxins in their venom with individual toxins shared with starfish, snakes and spiders.

As noted, they are egg-laying mammals: monotremes. This literally means “one hole” — clinically describing the single shared urinogenital tract that combines digestive, reproductive, and excretory systems to receive (female and gay platypuses) and expel (male) sperm, urine, feces, and eggs (female).

Their duck bill is not like a duck at all: it’s an electrical “radar” system full of skin and nerves: they forage for food in water with their eyes closed and capture prey through electrical impulse receptors. A duck’s bill is just a large scoop made of beta keratin (human hair & rhino horns are alpha keratin).

Everything about them is unique. But Australia is a uniquely deadly environment. So I have no idea how or why they are what they are.

Blogger David Fenger February 07, 2019 4:01 PM  

@95 It doesn't negate my observation to note that fixation rate is also inversely proportional to population size. Vox's calculations didn't take population size into account, so I was working with the assumption that the population size was fixed.

Just as a quick mental experiment: two populations of bacteria, both the same size. Population A is exposed to high radiation levels, causing 10x as many mutations. Population B is the control.

Will Population A have more fixed mutations than Population B over a long span of time to average out random fluctuation? I submit that the answer is yes, and by and large one would expect to see 10 times as many fixations, since the pool of mutations available to be fixed is ten times as large.

To be more mathematical about it: assume Population A acquires 100,000 mutations, and Population B acquires 10,000 mutations over the experiment. If the probability of fixation of any given mutation in that time frame is 1 in 1000, then one would expect A to fix 100 mutations and B to fix 10.

That probability of fixation will vary based on population size, but the above example makes it clear that the quantity of fixed mutations will also depend on the rate of mutations.

Blogger Sammi Hass February 07, 2019 4:15 PM  

I just mutated into a berserkr and not until my rage is saited will I rest.

Blogger Xiety February 07, 2019 4:20 PM  

Respect.

Blogger Azure Amaranthine February 07, 2019 4:24 PM  

"I was working with the assumption that the population size was fixed."

That would logically remove a lot of the reasons something would become fixed in the first place, such as adaptive pressures or increased reproductive rate.

"Will Population A have more fixed mutations than Population B over a long span of time to average out random fluctuation?"

Not unless population B's "mutation" (assumed beneficial) rate is lower than the potential fixation rate, which you should note from your wikiwalking isn't going to be the case unless the population is extremely small.

"and by and large one would expect to see 10 times as many fixations"

Not necessarily. One might expect more mutations within a single fixation, but not more fixations unless you have either a rapid succession of X-men style killer mutations like Gariepy mentioned, which is both an extraordinary assumption and would play havoc with your assumption of a fixed population size, or a rate of mutation in population B quite a bit lower than what is actually observed for anything I'm aware of.

"since the pool of mutations available to be fixed is ten times as large."

Fixation implies that it propagates to the entire population. Parallel fixation is possible, but each mutation is also to some extent in competition with other mutations. More importantly, the vast majority of the mutations are detrimental even after assuming some are strictly beneficial.

" If the probability of fixation of any given mutation in that time frame is 1 in 1000, then one would expect A to fix 100 mutations and B to fix 10."

It's more complex than that. If mutation M propagates from individual N, that individual's offspring must assimilate the entire population for the mutation to become fixed. Any mutations coming from other individuals must either overcome or become co-located in a manner of speaking with M in order to be fixed as well. Each successive mutation to be fixed raises the bar for how contorted reproduction patterns must be to co-locate, and at some point the pressure is higher than the generational rate can sustain. Only so many mutations occurring in different individuals can be fixed within a given population size within a given amount of generations.

"but the above example makes it clear that the quantity of fixed mutations will also depend on the rate of mutations."

Only if mutation rate is extraordinarily low or mutations are extraordinarily impactful.

Blogger OGRE February 07, 2019 4:25 PM  

@90 Blastman

There is no scientific observed evidence of the building up of new and novel genetic functions and features going on.

Exactly. This has always been my issue with TENS. The evolutionist builds up from his observations that species mutate into ways that eventually adapt better to a given environment. But it seems more likely to work the other way...that a given environment suppresses (or even destroys) already existing biological information. Organisms don't adapt TO an environment, they either survive the environment, they flee the environment, or they die. Introducing a species to a new environment does not introduce new genetic information into the species, but genetic information that may have been suppressed in the previous environment might flourish in the new one, and genetic information that worked well in the old environment might be hazardous in the new one.

But they have yet to demonstrate a single instance of a 'mutation' that creates a new way of interacting with an environment. Its one thing to observe beaks getting longer or coloration patterns becoming more prominent; its a completely different thing to introduce information that would produce new organs or appendages. Until they can offer evidence on how new information springs into existence ex nihilo I see no reason to conclude anything beyond the environment suppresses inefficient genetic information.

Blogger Passionate Observer February 07, 2019 4:25 PM  

Poe's Law wins again.

Blogger Azure Amaranthine February 07, 2019 4:26 PM  

I should rephrase by removing "(assumed beneficial)". It isn't necessary.

Blogger Azure Amaranthine February 07, 2019 4:28 PM  

"Poe's Law wins again."

Pigpanzee.

Blogger The Deuce February 07, 2019 4:38 PM  

I'm still waiting for Passionate Observer to expound on "the relatively recent discoveries of at least half a dozen additional mechanisms for creating genetic changes" that he so famously asserts that he has special knowledge of that eludes most career biologists.

So far he's named exactly one: mammals having sex with birds and making babies.

Which is a completely retarded idea.

And he tried to justify it by quoting a career biologist (which apparently go from being outdated idiots to rock-solid authorities the moment Pompous Observer wants them to be) pointing out some basic uncontroversial facts about hybrids, as if the mere existence of ligers proves that Rover and Daisy can build a literal nest egg together.

But I'm sure that was just the weakest and most speculative of the half a dozen or more new mechanisms of genetic change Pissant Observer is privy to, and the remaining 5+ will just blow our minds with the sheer enlightenment of it all.

Blogger VD February 07, 2019 4:39 PM  

It's tragic, but not surprising, that this blog is a place where you're unable to accept complements for honorable behavior without exposing yourself to danger.

And the Gamma goes to 11!

Blogger Azure Amaranthine February 07, 2019 4:42 PM  

"But I'm sure that was just the weakest and most speculative of the half a dozen or more new mechanisms of genetic change Pissant Observer is privy to, and the remaining 5+ will just blow our minds with the sheer enlightenment of it all."

There comes a point where, once you recognize a certain sort of individual, you understand that there's no point to arguing and you should either leave or take joy in the beating, if that is your wont. Pearls before pigpanzees you know.

Blogger Blastman February 07, 2019 4:42 PM  

If the ratio of beneficial to deleterious mutations is 1-100, then for the purposes of evolution, the number of relevant mutations would be 100x lower than those cited. 1-1000, it would be 1000x lower.

I suspect the evolution mutation numbers include all mutations, where only the beneficial ones are relevant for any evolution discussion.

Anonymous Anonymous February 07, 2019 4:50 PM  

The genius of Stephen Meyer's tilt at the neodarwinian windmill is that he actually went and read Darwin, who proposed that his theory was built on a specific proposition.

That proposition is the philosophic basis of uniformitarianism, the claim that we can only explain events in the past by recourse to processes we see going on around us in the present.

This was the "Deep Time" crowd's response to catastrophism and/or steady state unversers (depending on who they were arguing with at the time), with catastrophism being a largely forgotten idea that has since become so uncontroversial it is now touted by the neodarwinians as one of the engines of evolution, and steady state universe being utterly forgotten in the detritus of Big Bang triumphalism.

Nonetheless, Meyer observes that in the processes we observe occurring in the present, there is only one that produces new information.

It is not random undirected natural forces:

It is intelligence.

Ergo ...

Blogger One Deplorable DT February 07, 2019 4:54 PM  

@107 - And he tried to justify it by quoting a career biologist...pointing out some basic uncontroversial facts about hybrids, as if the mere existence of ligers proves that Rover and Daisy can build a literal nest egg together.

Love wins!

Blogger FUBARwest February 07, 2019 5:08 PM  

While we wait for PO to give us all this new information we plebz aren't privy too, l with all the information we have about genes and adaptation to the environment shouldn't the conclusion lean towards evolution being a process of regression and not progression?

Also, iirc, Darwin himself said his theory was bupkis if we ever found a biological mechanism whose parts couldn't evolve independently.

Blogger Snidely Whiplash February 07, 2019 5:10 PM  

This comment has been removed by the author.

Blogger David Fenger February 07, 2019 5:10 PM  

@102 The whole point in holding the populations fixed is to remove that variable from the calculation. That, and Vox didn't consider it above, so I'm free to ignore it now.

For the mental experiments, Population A and Population B are identical except for the introduction of a higher mutation rate in Population A. Same size, same probability of fixation of any given mutation.

I am not discussing beneficial or even visible mutations. For the purposes Vox is using above (using genetic drift as a clock), the bulk of the mutations in question are silent, so there's no competition as such.

I agree that one can't treat the mutations entirely in isolation, but it's not as bad as you're making out. First, each chromosome can fix independently. Second if one considers the history of a specific mutation that fixes, it will spend the bulk of its time expressed in a tiny fraction of the population, unaffected by the rise and fall of other mutations. Third, the pool of chromosomes with mutation X on them will be subject to further mutation, so for a 'common' mutation (say one that's most of the way to the finish line and present in 10% of the population), there will be numerous other mutations on that same chromosome, at varying prevalences. They all have a last common ancestor X-thousand generations ago, but the same mutation and fixation argument that applies to the population as a whole, also applies to them.

And none of that matters. It's still linear. If 40,000 replications of bacteria produce 25 fixed mutations, then 45,000,000 replications (not generations) in mammals seems likely to produce around 28,000. Except the mammalian genome is three orders of magnitude larger, and thus going to see a proportionately larger mutation rate. (This has been measured by direct genetic methods, by a study also mentioned in the article I liniked.)

Vox's numbers are way, way out, and the corrected values are of similar order of magnitude to the number of mutations observed, which is about as good as one expect do for back of the envelope work.

Blogger Snidely Whiplash February 07, 2019 5:15 PM  

David Fenger wrote:Just as a quick mental experiment: two populations of bacteria, both the same size. Population A is exposed to high radiation levels, causing 10x as many mutations. Population B is the control.
Or. more likely, most of the population is killed by the mutations caused by excessive radiation, except those individuals that have better DNA repair mechanisms. the smaller population with better DNA repair mechanisms results in a population with a much smaller variance in genotype.

Blogger David Fenger February 07, 2019 5:17 PM  

@116 I'm assuming a competent experimentalist that can pick a radiation level that doesn't induce massive die-offs of the bacteria.

Blogger Snidely Whiplash February 07, 2019 5:51 PM  

Mutations themselves are overwhelmingly fatal. The more complex the organism, IOW, the more allels, the more dangerous mutations are.
Your assumption is specifically invalid. If the radiation or other mutagen level is sufficient to increase the number of mutations by 10x, it will be sufficient to increase the death rate from mutation by 10x. It will also increase the rate of unsuitablity by 10x. Given that mutations are 10:1 harmful to beneficial, the overwhelming effect of increasing mutation will be harmful.

c.f. https://www.sas.rochester.edu/bio/people/faculty/fry_james/assets/pdf/fry_publications/Fry_genetics_Mukai_04.pdf

Blogger Snidely Whiplash February 07, 2019 6:00 PM  

No, overwhelmingly fatal is an exaggeration. Overwhelmingly deleterious is a far better statement.

Blogger Azure Amaranthine February 07, 2019 6:14 PM  

" For the purposes Vox is using above (using genetic drift as a clock), the bulk of the mutations in question are silent, so there's no competition as such."

That's not how it works. Transference with genetic drift as your mechanism means a longer time to fixation, if it occurs at all. It doesn't mean they aren't competing, it just means there's less internal pressure to fit within a given time frame because, again, longer time to fixation. However, longer time to fixation also means less fixations in a given time.

"First, each chromosome can fix independently."

I'm not using "co-located" in the same sense as you're thinking. I mean that both mutations have to be carried by all individuals eventually, and this can't happen very fast, or ever in some cases, without very specific reproductive patterns.

" Second if one considers the history of a specific mutation that fixes, it will spend the bulk of its time expressed in a tiny fraction of the population, unaffected by the rise and fall of other mutations."

Irrelevant either way. Unless, again, the mutation rate is far, far lower than what we observe.

"Third, the pool of chromosomes with mutation X on them will be subject to further mutation"

Already accounted for, which is why I said mutations arising in other individuals.

"so for a 'common' mutation (say one that's most of the way to the finish line and present in 10% of the population)"

10% saturation is not most of the way to the finish line unless you assume exponential saturation, which you can't, via genetic drift. Anyway, moving on.

"but the same mutation and fixation argument that applies to the population as a whole, also applies to them."

Again, anticipated, which is why I said in different individuals.

"And none of that matters. It's still linear."

"It", mutation to fixation proportionality, is not linear. It may appear to be linear at certain scales, but it is not.

"If 40,000 replications of bacteria produce 25 fixed mutations, then 45,000,000 replications (not generations) in mammals seems likely to produce around 28,000. Except the mammalian genome is three orders of magnitude larger, and thus going to see a proportionately larger mutation rate"

Except the fastest bacteria we know of, per Vox and Gariepy, produce one fixed mutation in that, so the mammalian would be around 500-5,000 in that many generations and 45,000,000 replications in mammals is, even if we use the notoriously short lifespan of a shrew, nearly twelve million years for 500-5,000 fixations, in a game where you need to show at least twenty five million to be allowed a seat at the table for the transition from proto chimp/human to either human or chimp.

You've got less than 600 million years for transition from single cell to human, and the math is saying you won't be a noticeable fraction of the way of the very last step of that. Even if I allow you the 28x speed you want, you're at only about 30% of the fixed mutations you need for the single step. And before you try to argue parallel, recall that we're already using rate of fixed mutations, not rate of fixation of mutations.

Blogger Azure Amaranthine February 07, 2019 6:16 PM  

"I'm assuming a competent experimentalist that can pick a radiation level that doesn't induce massive die-offs of the bacteria."

You're literally asking for an Intelligent Irradiator to drive evolution for you? K....

Blogger Avalanche February 07, 2019 6:59 PM  

@98 "Their duck bill is not like a duck at all: it's an electrical "radar" system full of skin and nerves"

Apparently, they also have a huge part of their brain dedicated to "smell" -- and there is a investigative thread of 'perhaps they can also SMELL underwater!' (Or perhaps sort chemicals... -- approximating smell?) Too-cool little beasties!

Blogger Kristophr February 07, 2019 7:02 PM  

Nice work Vox. It looks like some paleo-biologists need to actually learn math.

About time, I think.

Blogger maniacprovost February 07, 2019 7:15 PM  

At this rate I expect Vox to prove TENS by mid next year.

in the processes we observe occurring in the present, there is only one that produces new information.

It is not random undirected natural forces:

It is intelligence.


Corporate outsourcing specialists disagree. 1000 contractors at 1000 workstations, given some selective pressure, generate new SKUs once or twice a week. Granted, the ratio of deleterious mutations is high.

Blogger David Fenger February 07, 2019 7:50 PM  

@120 "Transference with genetic drift as your mechanism means a longer time to fixation, if it occurs at all."

That's as may be, but that is exactly what the experiment was measuring. Vox's argument is built on the measurement of the rate at which neutral mutations fix in populations of bacteria and hominids. It's not a great comparison for many reasons, but it's the numbers presented, so I'm working with what we have.

"Except the fastest bacteria we know of, per Vox and Gariepy, produce one fixed mutation in that, so the mammalian would be around 500-5,000 in that many generations and 45,000,000 replications in mammals is, even if we use the notoriously short lifespan of a shrew, nearly twelve million years for 500-5,000 fixations."

The 40,000 replications to 25 fixation number comes from Vox, above, and the paper I cited.

Vox's number is 9,000,000 years since CHLA. 20 years per generation = 450,000 generations. However! Every generation takes approximately 100 cell-replications to go from zygote to person to zygote again. So 9 million years of hominid evolution represents 45 million *replications*, which are where most mutations get introduced.

This is cross checked in the cited paper. Based on genetic sequencing of parents and children, the mutation rate is 10^-8 per base pair per generation, 100x that of the 10^-10 base pair per generation rate in the bacteria.

The bacteria genome is 5 x 10^6 base pairs. Humans are 3 x 10^9. Thus, about 100,000x the mutation rate per generation.

"Mutation to fixation proportionality, is not linear. It may appear to be linear at certain scales, but it is not."

I agree that there are non-linear parts of the curve, especially as the mutation rate get high. I'd like a little more than your say-so to show that humans are in the nonlinear region. After all, from where I sit it appears that the linear model holds nicely between bacterial and human scale.

Can you cite a source for that nonlinearity, please? A model, an equation, anything that I can use to get relevant numbers for this discussion.

Blogger justaguy February 07, 2019 8:00 PM  

The probabilities are so enormously stacked against TENS. This has been known since the 1950s when we first began to recognize the complexity of protein chains. The only issue is working the argument to define the terms and try to set the bounds of the assumptions but it becomes hugely improbable for any changes to stack up in the timeframes available. Lots of work needs to be done-- JP is simply trying to finesse a way around the numbers with "replicators".

Blogger Cloudbuster February 07, 2019 8:14 PM  

FUBARwest wrote:"Both JF and Vox are totally out of date in both your arguments. The field of evolution has passed you by. Suggest you read When Evolution Stops."

Second or third time you've said this. Say what you think is so relevant.


That would require him to put up or shut up, and we know that's not going to happen.

Blogger Cloudbuster February 07, 2019 8:26 PM  

FUBARwest wrote:"Both JF and Vox are totally out of date in both your arguments. The field of evolution has passed you by. Suggest you read When Evolution Stops."

Second or third time you've said this. Say what you think is so relevant.


I took a quick look at the "Look Inside" for When Evolution Stops on Amazon. It's never had a single reader review. It's 165 pages. The look inside doesn't allow you to see anything but the Introduction and the Table of Contents, but it's not promising, from what little you can see. I'm not inspired to spend $6 on the Kindle edition. It has the feel of a crank who's become deeply fixated on his pet theory.

Blogger Sammi Hass February 07, 2019 8:29 PM  

I found an article by that author of When Evolution Stops. It's mostly literature review based around the idea that cataclysm drives evolution. This theory is also known as punctuated equilibrium. Nothing novel here. Maybe the full length book has more to say but I'm not biting.

https://www.researchgate.net/publication/322243600_MASSIVE_VOLCANISM_AND_EXTRATERRESTRIAL_IMPACTS_AS_THE_SOURCE_OF_EVOLUTION

Blogger pyrrhus February 07, 2019 11:47 PM  

@129 The problem with Gould's punctuated equilibrium theory is that, apart from hybridization, which happens a lot but doesn't usually result in new species, there's no DNA rationale for it.

Blogger pyrrhus February 07, 2019 11:49 PM  

A measure of how weak the theory is for new species is the volume of mindless vituperation directed at anyone who points out the massive problems, which Darwin himself was aware of...

Blogger bodenlose Schweinerei February 08, 2019 1:22 AM  

By the way somthin'. Sammi, how are your complements? Do you get many compliments on them?

Blogger Azure Amaranthine February 08, 2019 2:05 AM  

"However! Every generation takes approximately 100 cell-replications to go from zygote to person to zygote again. So 9 million years of hominid evolution represents 45 million *replications*"

Please. You know perfectly well that for this calculation "replications" are full generations. Nice try, but that was a poor evasion attempt. If you want to use hominids I'm now going to use a time to replication cycle of twelve years per generation, and this is still being very lenient with you in the face of the 20 you just stated, instead of the ninety days I was estimating with shrews.

"The bacteria genome is 5 x 10^6 base pairs. Humans are 3 x 10^9. Thus, about 100,000x the mutation rate per generation."

You don't seem to realize that by going off of the 5,000 in "500-5,000" and then giving you your 28x multiplier I've already given you a rate of 140,000x. I'm now going to go off of the 100,000x, reducing your bonus multiplier.

"Can you cite a source for that nonlinearity, please? A model, an equation"

Literally already gave you the model. If mutations can compete in any way whatsoever with each other, including being variant mutations at the exact same site, it obviously cannot be exactly linear.

Congratulations, your finished equation just went from 30% of the singular step from proto-chimp/human to chimp or human over 600,000,000 years, to 0.44%.

Blogger SirHamster February 08, 2019 3:08 AM  

David Fenger wrote:The bacteria genome is 5 x 10^6 base pairs. Humans are 3 x 10^9. Thus, about 100,000x the mutation rate per generation.

On the flip side, bacteria have between 30 minutes to 12 hours (720 min) per generation, compared to 15-20 years (7.88 - 10.5 x 10^6 min) for humans.

Using the max and min for each range (7.2x10^2 vs 7.88x10^6), you're looking at a 10^4 ratio for time per generation. That reduces the mutation rate advantage of humans to 10 times that of bacteria. That's at best. Using the other side of each range, humans accumulate mutations at roughly the same rate as bacteria.

But you have a genome that is 10^3 larger, so even the best case 10^1 higher mutation rate does not keep up with the higher mutation requirements for evolutionary advancement.

Exponents are a bitch for all unguided evolutionary theories.

Blogger SirHamster February 08, 2019 3:17 AM  

Don't forget that all of these models are assuming positive mutations only.

Negative mutations work against positive mutations. Simply assuming that positive/negative mutations are 1:1 and NS does not weed out 100% of negative mutations destroys evolutionary progression rates. The evolutionary models must include possibility of failure and extinction in order to be representative of reality.

Unsurprisingly, evolutionary believers don't do this homework, at all. Why wouldn't they crunch the math, since it should support evolutionary theory?

They. don't. want. to. know.

Blogger Станислав Бартошевич February 08, 2019 4:16 AM  

@67
If a mutation provides an organism with a reproductive advantage over its peers, it can become fixed in a population within a single generation.

All you have to do is to explain how a mutation that provides an organism with a reproductive advantage substantial enough to be detectable by natural selection may actually occur, without resorting to Resident Evil biology, and then explain away about half or more of higher organisms on Earth, which proudly bear all sorts of reproductively disadvantageous traits.

For example, a single hominid smart enough to manufacture spears could arm his kin or tribe, kill the males of every other tribe in the geographical vicinity, and establish his genetics as a significant proportion of his species' genome within a single lifetime;

Slightly rewording a comment from one of the previous threads, do you understand at how many zeros we'd be looking when trying to calculate a mathematical (im)probability of a gene coding the IQ jump you postulate just writing itself by random chance in a single generation (gradual writing by accumulation of DNA changes over several generations would only add more zeroes, because until complete the gene in question will confer no advantage, will be invisible to natural selection, and prone to removal from population by random chance).

Blogger Станислав Бартошевич February 08, 2019 4:28 AM  

@56
Some moronic geneticist who wasted a three decade career studying hybridization:

"Moreover, in mammalian hybrid crosses, the male hybrids are usually more sterile than are the females. In a commercial context, this fact means that livestock breeders typically backcross F₁ hybrids of the fertile sex back to one parent or the other. They do not, as a rule, produce new breeds by breeding the first cross hybrids among themselves. Often, even after a backcross, only the females are fertile among the resulting hybrids. So repeated backcrossing is typical. Commonly there are two or more generations of backcrossing before fertile hybrids of both sexes are obtained and the new breed can be maintained via matings among the hybrids themselves. More backcrossing tends to be necessary in cases where the parents participating in the original cross are more distantly related."


So, hybridization (between closely related animals, unless you can point as to breeders who work with any others) requires VERY CAREFUL selective breeding to stick.

A nice argument for intelligent design you got here, although I'm not sure if it improves much on common sense observations.

Anonymous Anonymous February 08, 2019 7:23 AM  

To put the mathematics in perspective, see the YouTube vid titled

Origin: probability of a single protein forming by chance

The numbers are quite ... interesting.

Blogger Ryan G February 08, 2019 8:45 AM  

@138. Resident Moron - Do a deep dive on how flagellate bacteria work. That's what ultimately convinced me that, a minimum, intelligent design had to be involved with the creation of life.

No one would look at a Swiss watch and say it came into being by pure chance. Flagellate bacterium of orders of magnitude more sophisticated than that. Like the watch, there are razor thin margins in place between "working" and "not-working". Yet we're to believe that something with microscopic electrical motors, complicated energy delivery pathways, and the ability to self-replicate 'just happened'. But a watch that is nothing more than specifically shaped lumps of brass and steel? Well, that's clearly something manufactured. It makes no sense.

Blogger John rockwell February 08, 2019 8:49 AM  

Most mutations are due to the corruption inherent in a fallen universe.
(Romans 8:20-21)

Anonymous Anonymous February 08, 2019 10:56 AM  

Hi Ryan

As a psychological study, the determined application of mutually exclusive standards is an interesting topic.

You get the same thing across many topics, from people with emotional attachment to political positions instead of intellectual commitments to moral principles.

Blogger Sammi Hass February 08, 2019 11:27 AM  

bodenlose SchweinereiFebruary 08, 2019 1:22 AM
By the way somthin'. Sammi, how are your complements? Do you get many compliments on them?

I don't recall ever getting complimented on my compliments and if I did I would stick my nose in the air, flip my hair, and walk away because that's sycophantic behaviour hahaha. I wasn't even aware Passionate Observer complimented me, and to be frank I was disgusted with that sycophantic "be my white knight" call out.

Blogger David Fenger February 08, 2019 12:20 PM  

@143 I re-checked the link, and it still seems to work for me. Check your script blocker, maybe? Link: http://book.bionumbers.org/what-is-the-mutation-rate-during-genome-replication/

I found the above via searching on the terms Vox provided. It's not the actual 40,000 generation study, but a well-documented article discussing that study. It does link the abstract of the bacteria study, and if you have an academic account you should be able to go from that to the full thing.

Following the links, this appears to be the full article:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3246271/

The above is about the sequencing of genomes, the scientists got the bacteria from an evolutionary experiment also documented in Nature, 2009. I can't find a full copy of the article (I'm not paying $9 for it), but the abstract sounds fascinating:
https://www.nature.com/articles/nature08480

Blogger David Fenger February 08, 2019 12:54 PM  

@133 I am not evading anything. Mutation rates are per replication, as most mutations happen when the cell divides and the genome has to be transcribed. From the literature, the transcription error rate seems to be about 10^-10 per base pair copied. Which is pretty fantastic, when you think about it. So the rate of *mutation* per *generation* depends on the number of replication events to get from a zygote to the successor zygote.

The mutation rate for humans has been studied via the same genetic techniques (see the paper I linked in @60 and again in @144), and the per-generation mutation rate is exactly in line with the numbers I'm giving you here. They give a "per generation base pair mutation rate of 1.2x10^-8 and 1.0x10^-8 in the CEU and YRO trios, respectively". This is slightly more than 100x the 8.9x10^-11 per generation per base pair rate in the bacteria study.

"You don't seem to realize that by going off of the 5,000 in "500-5,000" and then giving you your 28x multiplier I've already given you a rate of 140,000x."

Source for your 500-5000 number? You mentioned it earlier but it's not in the study.

"If mutations can compete in any way whatsoever with each other, including being variant mutations at the exact same site, it obviously cannot be exactly linear."

How non-linear? Because it matters a lot. If 100,000x mutation rates per generation produce 100x the fixation rate, we'd get 125x100 = 12,500 mutations, three orders of magnitude short of the amount expected for the human ancestry path. But if it's only 50% lower, 50,000x the fixation rate, then we're close enough for back-of-the-envelope work.

Your argument entirely relies on this point. It entirely contradicts the Wikipedia article on fixation: "Thus, the rate of fixation for a mutation not subject to selection is simply the rate of introduction of such mutations."

There's my cite. Where's yours?

Blogger Wild Man February 08, 2019 1:12 PM  

@143 - thank-you David. I see that I originally glossed over your comment #66 (where YOU did provide the link to an article discussing the 2009 Nature study VD is referencing). Your interpretation of the article you linked is straightforward. And so, for his own credibility-sake, VD needs to weigh in on your difference of interpretation with him, on this now.

Blogger Azure Amaranthine February 08, 2019 1:36 PM  

"Source for your 500-5000 number?"

Your desired three orders of magnitude over bacterial rate. You don't seem to understand. I'm literally letting you pick the numbers for many of these, and you just keep drubbing yourself over the head with increasing viciousness.

"How non-linear? Because it matters a lot."

No, it's absolutely irrelevant. Our gives fixation rate is already accounting for both parallel mutation and parallel fixation.

"Your argument entirely relies on this point."

You're retarded. I argued that because I felt like it, and it's blindingly obvious. You're not worth my time.

"Thus, the rate of fixation for a mutation not subject to selection is simply the rate of introduction of such mutations."

That's why it's Wikipedia. That statement is dirty-pants-on-head retarded. It's claiming 100% eventual fixation rate for a neutral mutation. This is a good illustration of why you aren't worth my time.

Blogger phunktor February 08, 2019 1:38 PM  

All of the proteinsof which the machine is composed had to exist before the first copy of the machine which creates them. So the issue is not numreric but causality. I’m forced to conclude”miracle”. If The Boss wants me to understand I guess He will put me a clue. Blessed is the name of the Lord.

Blogger phunktor February 08, 2019 1:53 PM  

From evolving inside fission reactors—
micrococcus radiodurans.



Blogger phunktor February 08, 2019 1:59 PM  

Homeobox

Blogger Azure Amaranthine February 08, 2019 2:06 PM  

Go back and watch the debate again David. All of your attempts at finding an out are already covered. If after another viewing you still don't get it, just give up and find something else to do as a hobby.

If this is your line of work, God help your employer because you should have been fired long, long ago, and should have chosen a different profession in the first place.

Blogger David Fenger February 08, 2019 2:07 PM  

@146 I don't see your point. The math, laid out as simply as I can:
Vox's estimate of fixed mutations for CHLA: 125.
Scaling rate for mutations per generation: 100,000x
Result: 12.5M fixed mutations, close to the 15M he mentions.

Ad hominem? That's where you're going?

The math in the Wiki article is a little counterintuitive, but fundamentally correct:
u = Mutations per organism per replication
Ne = Population size.

Probability of fixation is 1/Ne. (As you earlier noted, it's inversely proportional to population size.)

Thus: new mutations per generation: u * Ne.
Probability of those new mutations eventually fixing: 1/Ne
Mutations fixed per generation: (u * Ne) * (1 / Ne) = u.

The quoted paper gives the *measured* rate of mutation in humans as 10-100 per generation. (ie, measuring both parents vs offspring, they found around 30 mutations. The sample size was small, hence the large error bars.)

If we take 30 mutations per generation as the estimation, and look at CHLA:

450,000 generations
30 mutations per offspring = 30 fixations per generation (per the above)
450,000 * 30 = 13.5 Million. Again, easily close enough to the target 15 Million to negate Vox's argument.

Blogger Azure Amaranthine February 08, 2019 2:54 PM  

So, you can't follow collegiate level English, you can't do math, and you have no comprehension of basic logic or logical fallacies. You really shouldn't have time to waste doing things you are clearly so phenotypically unfit for. Now that I'm thoroughly bored, we're done here.

Blogger Wild Man February 08, 2019 2:57 PM  

Azure - what is wrong with Fenger's math in comment #151?

Blogger David Fenger February 08, 2019 3:12 PM  

@152 None of that comes close to a refutation of the math.

Show your work, I've shown mine.

Anonymous Anonymous February 08, 2019 3:16 PM  

Still waiting for the list of new sources of genetic information from Pigpanzee Obsessor.

Blogger SirHamster February 08, 2019 3:36 PM  

David Fenger wrote:30 mutations per offspring = 30 fixations per generation (per the above)

One tiny reason why you should know this is wrong: TENS requires negative mutations to get weeded out by Natural Selection.

1.) A 100% mutation fixation rate is not TENS.

2.) Assuming every single mutation is progress towards the next evolutionary phase is not random mutation. Shouldn't need to explain anything about the concept of positive/negative mutation.

Your model represents supernaturally guided genetic uplift, which no one is arguing for. Your model doesn't represent what you think it does, try again.

Blogger David Fenger February 08, 2019 4:05 PM  

@156 It is not a 100% mutation fixation rate. It is a 1/Ne fixation rate, exactly as expected.

To run the numbers with specific examples, numbers approximate but close:
Human mutation rate per individual born: 30
Human population: 7 Billion (plus or minus a few)
New mutations per generation: 210 Billion.
Odds of fixation of a given mutation: 1/7 Billion.
Number of those mutations that will eventually fix: 210 Billion / 7 Billion = 30.

Every generation repeats the above, and has the accumulated load of prior generations' mutations. So on average, every generation fixes 30 mutations.

The math above is for neutral mutations, ones that convey no change in fitness. Given the vast number of iterations required to go from mutation to fixation, even the tiniest advantage or disadvantage will massively change the average fixation rate. It's a bit like compound interest in that way.

Blogger Wild Man February 08, 2019 4:23 PM  

@156 - sirHamster - you said - "A 100% mutation fixation rate is not TENS"

You are probably reading Fenger inaccurately. Fenger is not implying a 100% mutation fixation rate. He is only implying that a species mutation fixation rate can be derived from the mutation rate per organism per replication, and the size of the population.

Blogger SirHamster February 08, 2019 6:06 PM  

David Fenger wrote:It is not a 100% mutation fixation rate.

My bad. Your 1:1 ratio of mutation/individual to fixed mutation/generation is absurd, but not directly contradictory to TENS.

It is a 1/Ne fixation rate, exactly as expected.

When you are assuming a higher fixation rate, what are you finding about that rate that is exactly as expected?

Odds of fixation of a given mutation: 1/7 Billion.

Vox used an experimentally observed mutation fixation rate as a starting point. Your 1 / 7 billion fixation rate is based on assuming that humans have vastly higher fixation rates than bacteria.


Bacteria, with their hour generation times and vast populations:
25 mutations / 40K generations

Humans, with 20 year generation times and much smaller population:
30 mutation / generation


Need better data to support that.

Blogger David Fenger February 08, 2019 6:27 PM  

@159 The probability of fixation for neutral mutations is proportional to the fraction of the population that has the mutation. It should be obvious that if half the population has variant A1, and half has A2, then there's a 50% chance that A2 will become fixed in the long run.

The same logic extends all the way down to a single mutation. There, the probability that a new mutation fixes is 1 (the population of that mutation) : Ne (the total population).

The rest is simple algebra. While it's counterintuitive that the result is independent of population size, the math is sound.


The data to support the assertion for bacteria and for humans are both found in the report I linked above. The rate of 30 for humans was measured using fundamentally the same method as for bacteria - full genome sequencing.

Blogger Up from the pond February 08, 2019 6:47 PM  

Thank you for crunching the numbers, Vox.

Blogger SirHamster February 08, 2019 7:07 PM  

David Fenger wrote:It should be obvious that if half the population has variant A1, and half has A2, then there's a 50% chance that A2 will become fixed in the long run.

Starting at 50% of the population is assuming a mutation that is growing dominant. 50% chance of what - fixing in the entire population by the next generation? in 10 generations?

50% of population is not 50% chance of fixation.


The rest is simple algebra.

Applying simple algebra to a calculus level problem introduces errors you cannot account for.

The rate of 30 for humans was measured using fundamentally the same method as for bacteria - full genome sequencing.

Measuring the differences between a single generation of human beings, parent and child, and treating all of those differences as fixed.

Using the same method as for bacteria for 40,000 generations of humans would take at least 800,000 years. Good luck running an experiment that long.

Being a little more generous and limiting it to 10 generations would still take 200 years.

Blogger carry_bit February 08, 2019 7:25 PM  

This comment has been removed by the author.

Blogger carry_bit February 08, 2019 7:41 PM  

Disclaimer: My biology education is limited to high school + Wikipedia. I have also not read the Nature bacteria study.

Question: Is the bacteria study actually an example of fixation in parallel?

Assuming the mutations are spread only by reproduction, for a mutation A to be fixed (100% occurrence), all living specimens must be descended from a specimen with the mutation. With only asexual reproduction, the fixation of two mutations A and B means that mutation B happened to an specimen that already had mutation A or vice versa (excluding the rare case where both happen at the same time). With sexual reproduction, a specimen can have both mutations by having one parent with only mutation A and the other parent with only mutation B.

If the time to mutation is much greater to the time of fixation once introduced, then asexual reproduction is essentially limited to serial fixation as the mutations in different specimens must compete with each other. Thanks to the two parent advantage of sexual reproduction, this restriction does not exist in that case and so parallel fixation is possible.

Going back to the summary, only with serial fixation is the 40000/25 = 1600 generations per fixation on average math is valid. With parallel fixation, by contrast, the 25 mutations could've all taken 39,000 generations to become fixed. This indicates to me that the Nature study was actually describing serial fixation.

Blogger David Fenger February 08, 2019 7:44 PM  

@162 SirHamster wrote:50% of population is not 50% chance of fixation.

It is exactly that. Not in one generation, no. But in the long run, there is a 50% chance the mutation will fix, and a 50% chance the mutation will extinguish.


SirHamster wrote:Measuring the differences between a single generation of human beings, parent and child, and treating all of those differences as fixed.

No, it measured between parents and child, and treated all the differences as *mutations*. This measures the mutation rate per offspring directly. Yes, it's a small experiment, but because the mutation rates for humans are high, it's possible to get useful numbers. In this case, something around 30.

This number tracks with the transcription error rate (10^-10 per bp per replication), the genome size of humans (3x10^9) and the number of replications per generation (~100). Multiply those together, the answer is the same as the experiment gives: 30 mutations (within suitable error bars).

It's the mathematics of neutral fixation that lets us go from 30 mutations per offspring to 30 fixations per generation. That the number also matches the CHLA numbers suggests it's in the right ballpark.

Blogger SirHamster February 08, 2019 7:50 PM  

David Fenger wrote:It is exactly that. Not in one generation, no. But in the long run, there is a 50% chance the mutation will fix, and a 50% chance the mutation will extinguish.

I had a question what you meant with 50% ... so thanks for elaborating.

David Fenger wrote:It's the mathematics of neutral fixation that lets us go from 30 mutations per offspring to 30 fixations per generation. That the number also matches the CHLA numbers suggests it's in the right ballpark.

You took a mutation rate measurement and then used an assumed fixation rate.

The bacteria measurement was fixation rate, not mutation rate. You are not comparing like things. Your fixation rate is not based on observation.

Blogger David Fenger February 08, 2019 8:41 PM  

@166 SirHamster wrote:You took a mutation rate measurement and then used an assumed fixation rate.

It does look a bit that way, but I've provided the math for why "neutral mutation rate per birth" == "fixation rate over whole population". So measuring the mutation rate per birth gives us the fixation rate.

Granted, there are some assumptions in the CHLA math:
1) Mutation rate now is similar to mutation rate over past 9 million years.
2) For most of the past 9 million years, human population levels were stable. (Violated in the past 3000 or so, but that doesn't affect the numbers noticeably.)
3) It ignores the impact of positive selection - the fraction of the mutations that improve survival will fix much faster and increase the fixation rate.
4) No survival bottlenecks.

I can't see any better alternatives to the above, though.

SirHamster wrote:Your fixation rate is not based on observation.

Interestingly, Vox has provided us with a natural experiment on human fixation rates. 15 Million fixed mutations over 9 million years.

# of generations: 9,000,000 / 20 = 450,000
# of fixations per generation = 15,000,000 / 450,000 = 33.33...

Oh look, there's that number again.

Blogger SirHamster February 08, 2019 8:55 PM  

David Fenger wrote:
It does look a bit that way, but I've provided the math for why "neutral mutation rate per birth" == "fixation rate over whole population".


Your math didn't apply to bacteria. Bacteria have more mutations than 25 / 40K generations.

Your fixation rate math is falsified in the general case. You have no evidence supporting it for the human case.


David Fenger wrote:Interestingly, Vox has provided us with a natural experiment on human fixation rates. 15 Million fixed mutations over 9 million years.

That's not an experiment. These sort of category errors is why your math is not impressive.

Blogger Crew February 08, 2019 10:48 PM  

Where is the number ~15M (or ~30M) coming from?

Is it something JF made up or cited somewhere?

Also, does it include SNPs and those genes that are known to be polymorphic in the human population?

See for example: http://cmm.ucsd.edu/varki/varkilab/Publications/B67.pdf

Where they claim "This problem is aggravated by
the fact that the genetic diversity of the great apes is
significantly higher than that in humans for many
genetic loci studied so far"

This is similar to Lactose Tolerance, which is not fixed among all humans, but is highly fixed among Northern Europeans.

Blogger Crew February 08, 2019 11:25 PM  

@167: Interestingly, Vox has provided us with a natural experiment on human fixation rates. 15 Million fixed mutations over 9 million years.

Where is that number of 15M coming from?

Is it based on some extrapolation of a measured rate?

Blogger Azure Amaranthine February 08, 2019 11:46 PM  

He's assuming the math on Wikipedia is correct, not realizing that it's a back-rationalization of what is assumed to have happened requisite to TENS or more specifically TEGD rather than experimentally or observationally verified. He's comfortable with that assumption because of observation bias, even though it heavily contradicts what is actually observed.

Not realizing that even if he managed 13.5m, that's a scenario where 100% of his mutations are beneficial or neutral, his fixation rate is many times higher than hypothetical catastrophic rate, you would be able to observe one new fixation per generation several times by now, let alone 30, and he still isn't reaching the requisite 15m even in this scenario.

Blogger Azure Amaranthine February 08, 2019 11:47 PM  

100% of his fixed mutations*

Blogger Crew February 09, 2019 12:01 AM  

Thanks. Which Wikipedia article? I looked at this one https://en.wikipedia.org/wiki/Fixation_(population_genetics) but no such number appears in it.

Is it JF who is assuming that number?

Blogger David Fenger February 09, 2019 12:34 AM  

SirHamster wrote:Your math didn't apply to bacteria. Bacteria have more mutations than 25 / 40K generations.

Bacterial mutation rate (from yet again, the same paper):
8.9x10^-11 mutations per base pair per replication.
The bacteria used has a genome of 5x10^6 base pairs.
Mutation rate per replication: 8.9x10^-11 * 5x10^-6 = 4.45x10^-4

Inverting that, we get 2250 replications to generate one mutation in bacteria. Which is pretty close to the one fixation per 1600 generations that Vox calculates above. Same equation holds, yet again.

So why do bacteria have a reputation for mutation? Cultured bacteria can easily reach 10^9 per mL, so in a tiny test reactor, they can try out millions of mutations per generation. That's what makes them dangerous - numbers. Individually, bacteria are much worse at generating mutations than humans. But in those numbers, all it takes is one with even a mildly advantageous mutation and they'll take off.

Blogger David Fenger February 09, 2019 12:52 AM  

@169 and @170 The 15 Million mutations is from Vox above. 30 Million differences between chimp and human genome (a quick google shows numbers in that range, I found a 40 Million reference easily), assign half to each branch from the least common ancestor 9 million years ago.

@171 There's no handwaving. The math is simple. The observations have been made via genetic sequencing - in the articles under discussion, even. The math works, as I've shown repeatedly.

If you have superior equations, citation please. I'd love to see them.

Azure Amaranthine wrote:you would be able to observe one new fixation per generation several times by now, let alone 30, and he still isn't reaching the requisite 15m even in this scenario.

What do you expect to see when a neutral mutation is fixed? The bulk of our DNA is non-coding, so most mutations don't even affect protein expression. If a neutral mutation fixes *nothing visible changes*. The only way to tell would be genetic sequencing of huge numbers of people. Even then, you couldn't be sure that the 'original' version of the gene isn't still being expressed in some random person you didn't test.

Fixation happens like science advances - death by death. If site A has two variants, A1 (original) and A2 (mutant), and A2 is present in everyone on earth but one, when that one person dies... nobody will notice. The 30 fixations that will happen in our generation will all pass unheralded, as everyone on the planet has the mutation already, except for the handful whose death will extinguish it.

And yet, over 9 million years (some estimates say 14 million, but Vox's number is better for his argument), 30 million changes between chimp and human have become fixed.


@173 Yes, that's the wiki article with the relevant equations. I'd have cited Infogalactic, but it has no mirror of that page.


Blogger Azure Amaranthine February 09, 2019 1:33 AM  

"The bulk of our DNA is non-coding, so most mutations don't even affect protein expression."

False. Non-coding just means that it is not directly copied into protein. 9-18% of our DNA is now known to regulate expression of the 2% coding, and around 60% more is estimated pending future study.

ENCODE is a good resource for a lot of this information.

Your required vast fields of TENS-workspace "junk DNA" does not exist.

Blogger David Fenger February 09, 2019 1:56 AM  

@176 New data to me. It would appear that your other 60% doesn't have a strong effect if they're having trouble figuring it out. Still, I'd rather not follow down that rabbit hole.

The equations get substantially more complex for mutations with a distribution of fitness values. It would simplify matters to assume that at least half of the mutations are close enough to neutral that the entire collection averages out to approximately the same rate.

Would you be willing to move forward with an assumption of 40% deleterious, 50% neutral, and 10% mildly advantageous mutations? I think I can come up with a reasonably simple model using that, or similar numbers if you'd care to name some.

Blogger SirHamster February 09, 2019 2:30 AM  

David Fenger wrote:Inverting that, we get 2250 replications to generate one mutation in bacteria. Which is pretty close to the one fixation per 1600 generations that Vox calculates above. Same equation holds, yet again.


The reason your equation holds is that you are reversing the calculation they made:

"Sequencing of 19 whole genomes detected 25 synonymous mutation (indicating neutral rather than selective changes) that got fixed in the 40,000 generations of the experiment. This measurement enabled the inference that the mutation rate is about 10-10 mutations per bp per replication in the measured conditions"

They measured what got fixed over 40K generations, and then assumed that the fixed rate corresponds to the individual mutation rate, and used that to calculate the mutation rate.

That means that your mutation rate and your mutation fixation rate are derived from the same observation. Treating the correlation between the two numbers as evidence of the mathematical relationship you ASSUMED in order to derive one of the numbers is circular reasoning.

Anonymous Anonymous February 09, 2019 5:39 AM  

David Fenger

Am I understanding this correctly?

You’re now arguing that 30 million neutral mutations is the difference between a man and a chimpanzee?

I ask only for clarity.

Blogger David Fenger February 09, 2019 9:58 AM  

@179 Not my argument. Taking Vox's data above at face value. I'd agree not all of them are neutral, but without having dug deep enough to find the numbers, I'm quite confident that over 90% are - and since I'm only trying to get the order of magnitude right, that's good enough. If you can find a research article that breaks those 30 million difference down into categories (Coding, coding-adjacent, non-conserved) I'd love to see it.

@178 Fair point, and I hoped someone else would notice. There are other lines of evidence pointing to roughly similar mutation rates, though digging into the literature I find that the number can vary far more than these two data points suggest.

The problem for your argument is that the math for fixation of neutral mutations makes their assumption entirely justifiable. They don't even examine that assumption in their work, and for good reason.

If you wish to argue that conclusion is wrong, when it results in a mutation rate that correlates well to other measurements (the human mutation rate is within 20% of the bacterial one at the base pair level), you need to address the math and the model.

I've seen some vague hand-waving about parallel vs serial fixation, but I haven't seen a mathematical presentation of the argument. As far as I can tell, that line of argument is entirely specious - fixation is obviously parallel.

Blogger Rocklea Marina February 09, 2019 10:49 AM  

That comes to 33 and a 1/3 mutations per generation propagating through the entirety of both species. Extended periods of population isolation and mating practices would mean the update packages could potentially contain thousands or more mutations at a time.

Blogger Rocklea Marina February 09, 2019 11:04 AM  

I'm going drink more Red Bull

Blogger Crew February 09, 2019 11:04 AM  

Bacterial mutation rate (from yet again, the same paper):
8.9x10^-11 mutations per base pair per replication.
The bacteria used has a genome of 5x10^6 base pairs.
Mutation rate per replication: 8.9x10^-11 * 5x10^-6 = 4.45x10^-4


You cannot compare prokaryote and eukaryote mutation rates.

Eukaryotes have superior repair machinery.

Anonymous Anonymous February 09, 2019 11:05 AM  

David,

I don't believe any mutations are neutral, nor that any are positive, even though some may confer temporary advantage in specific circumstances.

There is no evidence of any mutation increasing the information content of the genome, which is what is required for new features to form, while there is overwhelming evidence that mutations destroy information.

The problem with the term "neutral mutations" is that you have to understand that it means mutations having no immediate selective effect.

As noted, every newborn has such mutations. It has copying errors more or less randomly distributed throughout its genes. For most of us, most of the time, these have no (currently) measurable effect.

But breed that newborn to its twin sister and see the true nature of its mutations. Mutations are overwhelmingly negative in the aggregate, even as they are overwhelmingly selectively neutral individually.

This is so simple and obvious there is no reason anyone should fall for this linguistic sleight of hand. You cannot improve A Tale of Two Cities by randomly mutating the text. Nor can you increase your chances of improving it by merging two randomly mutated versions of the text. Nor 2,000,000 versions over 5,000 generations of mutation.

Firstly, IF there IS selective pressure, ie if the mutations are not selectively neutral, then natural selection works to stabilise the species around its norms. It eliminates the negatives. Ever pondered why evolutionists are troubled by the hundreds of millions of years of phylogenetic stasis they suppose they find in the fossil record? Well, that's what natural selection does. It eliminates the divergent.

Secondly, genetics doesn't work one gene at a time. The difference between a human and a chimp is not merely a different set of genes. Many of those genes have to be present in a specific network of inter-related structures or they don't convey any advantage, they don't build anything new, and thus at best they represent an organic burden having no benefit to justify its existence. More usually, transplanted into the wrong context they're deleterious. Again, natural selection across thousands of generations of large enough populations would eliminate both of these.

Finally, as noted, if you try to work TENS against very small "lucky" populations you run smack on into the problem that it becomes increasingly likely over time that in the real ("natural") world your small population will succumb to an earthquake, a volcano, a famine, a punitive raid, a disease, or inbreeding, and simply cease to exist at all.

The numbers simply do not work.

Blogger Crew February 09, 2019 11:28 AM  

@175: Well, I found this:

https://sandwalk.blogspot.com/2012/01/whats-difference-between-human-and.html

It concludes that things are consistent.

Note, it does take into account the differences in generation time over the length of the lineage that lead to homo, coming up with an average of 10 years, not 20.

However, that seems short to me, although I would think that generation times were shorter earlier on. In any case, the numbers are such that assuming an average generation time of 20 years still works.

The comments are interesting as well because of comments from a guy who wrote a freely available 600-page book on population genetics.

Blogger SirHamster February 09, 2019 11:29 AM  

David Fenger wrote:The problem for your argument is that the math for fixation of neutral mutations makes their assumption entirely justifiable. They don't even examine that assumption in their work, and for good reason.

Using circular reasoning to justify treating human mutation rate as human fixation rate is absurd.

David Fenger wrote:If you wish to argue that conclusion is wrong, when it results in a mutation rate that correlates well to other measurements (the human mutation rate is within 20% of the bacterial one at the base pair level), you need to address the math and the model.

I don't need to argue that a conclusion supported by circular reasoning is wrong.

Blogger David Fenger February 09, 2019 1:13 PM  

@186 The conclusion on humans may be wrong, but that part is not circular.

Step 1) The measured mutation rate in humans is ~30 per offspring (direct measurement via comparing parental and offspring gene sequences).
Step 2) The mathematics of neutral fixation state that fixation rate over the population per generation = mutation rate per organism.
Step 3) Thus, the fixation rate in humans is around 30 per generation.
Step 4) Comparing this number with the number of mutations and number of generations since the Chimp-Human Last Ancestor we get a match within an order of magnitude.

None of that is circular. If you wish to present a mathematical argument against step 2, I'm game.

Blogger David Fenger February 09, 2019 1:39 PM  

@183 Vox started the bacteria to human comparison. Fortunately, we have a direct measurement of the human mutation rate that (via neutral fixation math) gives us a result entirely compatible with the number of mutations since the Chimp-Human Least Ancestor. The article you found in @185 is great, thanks for that.

@184 It doesn't much matter what you believe. The research is pretty clear on the topic of neutral and positive mutations.

There are multiple kinds of replication errors. While most of the math above concerns point mutations, another common type is insertion or deletion of a sequence. The article Crew kindly linked above notes the 30 million for CHLA is the point mutation count. It also mentions insertion/deletion errors or "indels": "The latest studies indicate that humans and chimps differ by only 26,500 large indels".

So it's quite easy to increase the information content of a genome: duplicate a gene, then mutate the copy. This has been observed many times. (By comparing genetic sequences between chimps and humans, for example.)

A gene sequence is not like A Tale of Two Cities. The sequence that codes for a critical protein like insulin not only can mutate, but has - cows and humans have different versions of insulin, with different amino acids in various locations. They both still work well. On top of that, the coding between DNA and amino acids is redundant - many amino acids are represented by 4 or more possible DNA combinations. As a result, over half of all point mutations in a coding region have *no effect* on the resulting protein.

Resident Moron™ wrote:The numbers simply do not work.

Show me the numbers. My numbers and math work fine for the CHLA case Vox derides above. If you wish to counter them, you need to provide well-sourced numbers and math to back the argument up.

Blogger SirHamster February 09, 2019 2:59 PM  

David Fenger wrote:Step 2) The mathematics of neutral fixation state that fixation rate over the population per generation = mutation rate per organism.

You again take that assumption of "fixation rate = individual mutation rate" and pass it off as a conclusion.

Mathematics do not state anything. You started with an assumption and made an equation out of it.

That you then double back and use the equation to treat the assumption as a conclusion is circular. This is doubly stupid when you've already been called out on it.

David Fenger wrote:If you wish to present a mathematical argument against step 2, I'm game.

"against" is the completely wrong mindset.

The summary of what you've brought up is that you have a different model that gets the mutation rate the evolutionary timeline requires.

The difference between your model and Vox's model is that he uses an observed bacterial fixation rate. You use an assumption to treat the observed mutation rate for a single generation of humans as the long term fixation rate.

It's interesting that it gives the "right" answer for this particular problem of chimp-human divergence, but that doesn't in itself justify the assumption. That calculated fixation rate doesn't have the same evidential weight as an observed fixation rate.

Anonymous Anonymous February 09, 2019 3:29 PM  

"A gene sequence is not like A Tale of Two Cities. The sequence that codes for a critical protein like insulin not only can mutate, but has - cows and humans have different versions of insulin, with different amino acids in various locations. They both still work well. On top of that, the coding between DNA and amino acids is redundant - many amino acids are represented by 4 or more possible DNA combinations. As a result, over half of all point mutations in a coding region have *no effect* on the resulting protein."

Oh boy.

No, it's not like A Tale of Two Cities - it is many orders of magnitude more complex and delicate. It is far more easy to irretrievably break; dozens of orders of magnitude more so.

It doesn't matter at all that there are two variants of insulin in cows and humans. What matters is that there are an effectively infinite number of ways to mutate the relevant genes, and thus to effect the machinery that makes the insulin, but only a very very small number (like 4 divided by 10^164 is an exceedingly small number) of them actually work to make ANY variant of insulin. And if you break that insulin producing machinery, as random tinkering will incontrovertibly do, then natural selection maximally demotes your TENS candidate.

You don't need the actual numbers to understand this argument, but the numbers are huge and they're massively stacked against TENS.

As for your remarks about information increase, you don't understand the most basic principles of what you're discussing. The machinery to replicate an existing gene itself requires a massive increase in information. Such machinery is itself massively complex and does not simply lie around the pre-biotic soup waiting for a hopeful gene to stumble over it and fall in love.

For fuck's sake - all this hand-waving away of monstrously infinitesimal probabilities is tedious. You cannot slide up-hill merely by laying the ladder down over a 1-in-1-trillion slope, and you cannot overcome the impossibility of random changes effecting an increase in genetic information simply by appealing to larger numbers and more time. It doesn't work that way, and everything we've learned and are still learning about biology reinforces that fact more strongly every day:

It doesn't work that way.

The time required for even the most basic parts to form by chance guarantees the sun will go nova before anything useful to life, let alone life itself, ever exists.

Blogger David Fenger February 09, 2019 6:31 PM  

@190 I am not discussing the origin of life here, it's way out of scope. I simply want to discuss the math on the rate of mutation since the Chimp-Human Last Ancestor.

The human insulin protein is 51 amino acids long, so there are 153 base pairs in the coding region. Of the amino acids in the A-Chain, 12 are coded by 2 mRNA codons, the other 9 by 3 to 6. So in the A-chain, with its 63 possible point mutation sites and thus 3*63 = 189 possible single-point mutations, 41 do not change the coded protein.

So even in the middle of the insulin coding region, there's a 41/189 = 21% chance of a mutation being neutral. Better yet, we know that at least three of the amino acids in insulin can be substituted with at least one other, because bovine insulin varies in three amino acids and still functions. So the odds are better than 21%.

I'll grant that natural selection will kill off any child with a mutated and nonviable insulin gene. The odds of that gene getting hit are very small for any given child. 153 base pairs x 10^-8 mutations per base pair per generation = 1.53e-6, so about 1.5 per million births. And of those, over 20% will have no ill effects.

Resident Moron™ wrote:You don't need the actual numbers to understand this argument

As a matter of fact, you do. Because I've shown my numbers, and they look pretty good for random point mutations being neutral much of the time - non-coding regions are much less sensitive.

I am not hand-waving any infinitesimals. The numbers are large, obvious, and clear. Again:
1) Humans are *measured* as having 30 mutations per birth.
2) Mutations are predominantly neutral enough for the purposes of fixation rates.
3) Neutral mutation fixation rate per generation = rate of mutations per birth.
4) Thus, humans have 30 fixations per generation.
5) 9 million years at 20 years per generation and 30 mutations per generation produces 13.5 million mutations, very close to Vox's 15 million.

Again, I am not here to debate the origin of life. Focus on the mutation rate, please. I'm game to argue "mutations are mostly neutral" and the fixation rate math, but handwaving without numbers does not constitute an argument.

Blogger Rocklea Marina February 09, 2019 7:35 PM  

30 mutations per individual granted, is long way from showing a cumulative per generation shift, as they are neutral and therefore not fixed and definitely able to revert or change.

Blogger Crew February 09, 2019 8:09 PM  

"The bulk of our DNA is non-coding, so most mutations don't even affect protein expression."

False. Non-coding just means that it is not directly copied into protein. 9-18% of our DNA is now known to regulate expression of the 2% coding, and around 60% more is estimated pending future study.


You might want to look at this list of papers that argues against the Encode claims:

https://sandwalk.blogspot.com/2018/04/required-reading-for-junk-dna-debate.html

Further, see this very recent paper (2018):

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1590-2

It concludes:

The overall picture that emerges from this analysis is that the cell is a relatively inefficient machine, transcribing more DNA into RNA than it needs. Ever since the discovery of introns [54, 55], we have known that genomes contain large regions that appear to have no function. Based on the results described here, it appears that nearly 99% of the transcriptional variety produced in human cells has no apparent function, although most of these variants appear at such low levels that they cumulatively account for only 32% of transcriptional activity.

Blogger Crew February 09, 2019 8:30 PM  

There is no evidence of any mutation increasing the information content of the genome, which is what is required for new features to form, while there is overwhelming evidence that mutations destroy information.

See here: https://slate.com/technology/2016/06/the-monkeys-of-south-america-evolved-to-be-colorblind-perhaps-because-its-actually-an-advantage-for-them.html

Yet, with the exception of owl and howler monkeys, the 130 or so remaining species have one thing in common: A good chunk of the females, and all of the males, are colorblind.

This tells us how color vision evolves: Via sex chromosomes, at least among mammals.

Those female monkeys in South America that are not colorblind have two different variants of the same opsin genes on their separate X chromosomes. This is the same way that some human females are tetrachromats.

Among primates with color vision, a duplication event occurred, and they are relatively common (see how many repeats of the two different opsin genes there are on the human X chromosomes, and they are next to each other) then one of them change through a small number of mutations so that some individuals were now trichromats. That then proved so selectively useful for old-world primates it exists in all of them today.

There in no new information being generated here. Every program possible is inherent in the language it is coded in.

It is entirely conceivable that God designed a genetic system that could express the whole range of life we see today and even more, and just let it do what it could.

Anonymous Anonymous February 10, 2019 2:30 AM  

"There in no new information being generated here."

No, it is being lost.

But showing it is being lost is not explaining where it came from.

Blogger David Fenger February 10, 2019 2:56 AM  

@195 Duplications happens. Duplication + mutation of the duplicate = increased information.

Anonymous Anonymous February 10, 2019 3:59 AM  

"Duplications happens. Duplication + mutation of the duplicate = increased information."

Again: the capability to duplicate requires an immense increase in information. It doesn't just "happen". The machinery of duplication is complex and delicate. Random tinkering with it is not going to improve it.

Mutation of the duplicate is NOT increased information. There is no known process by which information arises spontaneously. As was pointed out to you earlier, you are assuming your conclusion and then using that assumption as if it is proof of your axioms. Your entire argument is utterly circular, i.e. invalid.

It is a trivially childish fantasy.

Darwin's entire argument was predicated on the claim that we can only explain current entities in terms of current processes. The only process currently known to give rise to new information is intelligence.

Therefore Darwin's own argument is self-refuting, because we now know that the information content of the genome is gigantic. It surpasses in information content and density anything (indeed, everything) we have been able to craft. The idea that it arose and increases itself by random natural processes is idiotic.

But even if it weren't, we KNOW that it does not. There is not a single example of information arising from any process other than intelligence.

Darwinism is a theory of the gaps - it relied for even the tiniest shred of plausibility on almost complete ignorance of how biochemistry actually works. Now that gap in our knowledge has been filled and darwinism is dead.

Blogger Azure Amaranthine February 10, 2019 4:12 AM  

"You might want to look at this list of papers that argues against the Encode claims:"

Only against the extra estimate of 60% based on utilization. The 9-18% regulating the "library" is not argued against as far as I see.

As with anything controversial, regardless the reason for controversy, we can expect to see refutation attempts. The term "junk" is not objective. It is not even even orthodox to their own beliefs, considering they believe it to be a sort of "workspace" for producing and trying new random sequences. It is rhetorical. The information may or may not be sound, but the middleman collating it is biased.

For my part, I observe that our understanding of ourselves is poor, and even if it were entirely non-functional space, this would also be expected if it were either the results of the devolution of now-unknown functions, or redundancy implemented to reinforce particularly fragile or important functions (which would be my first assumption for most of it, considering the repetition).

"See here: https://slate.com/technology/2016/06/the-monkeys-of-south-america-evolved-to-be-colorblind-perhaps-because-its-actually-an-advantage-for-them.html"

That is indeed the exact opposite of an example of increased information or function. Niche-useful, yes, but if it is fixed it is a permanent loss of flexibility and function for a temporary advantage.

"It is entirely conceivable that God designed a genetic system that could express the whole range of life we see today and even more, and just let it do what it could."

Better yet, blanket solutions capable of self-differentiating into divergent niches. A measure of antifragility even in the face of a system falling to pieces around them.

Blogger Azure Amaranthine February 10, 2019 4:20 AM  

" Duplication + mutation of the duplicate = increased information."

Only if it's useful. Two can play the "trash" game.

Blogger SomeOne February 10, 2019 7:51 AM  

Azure, I have read the entire thread in order to follow your and David Fenger's arguments - just thought you should know your efforts are of value.

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