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Saturday, February 16, 2019

In full retreat

The defenders of the Neo-Darwinian hypothesis of evolution through natural selection and a whole host of things that have nothing to do with natural selection are frantically fighting a rhetorical withdrawal as they attempt to deal with the problem of the average rate of mutational fixations over time.
Torin McCabe: Vox first you said you could use math equation using fixation rates to disprove evolution since there is not enough time.  People called BS saying you could not use those rates. Next you say that we should be able to see differences in historic DNA and yes of course scientists are looking into that but again you are jumping gun if you assume that the rate of change is uniform across time.  For example 80% of the change could have occurred in 20% of the time leaving long periods of relative stability.  So regretfully your case cannot just be proved by showing how human DNA was relatively static for 100,000 years of a 12 million year period.  It will look very strange if we find DNA that narrows all the change to a very short period of time; and then perhaps external influence could then be an interesting hypothesis.


Vox: We can and it increasingly looks like we will. The defenders of the Neo-Darwinian hypothesis are losing the scientific battle, losing badly, and you know it because you're attempting to retreat to a position of "well, it could have all happened super fast in the one area that we can't examine yet."  And even that retreat fails to account for the fact that we should be seeing more and faster fixated mutations among the human race further separating us from the CHLCA because a) beneficial mutations fixate faster among growing populations and b) the environmental changes have been greater over the last 450 years than at any time previous, including catastrophes and Ice Ages.

The Neo-Darwinian hypothesis has not been conclusively falsified, not yet, but the probability that it will be is rapidly increasing with advancements in genetic science. And with every retreat to "yeah, but I can imagine that this thing we haven't ever observed is still theoretically possible", more and more people are rhetorically convinced that the Darwinian emperor has no clothes.

It doesn't help when you tell ridiculous lies like: "again you are jumping gun if you assume that the rate of change is uniform across time". I have never, ever assumed any such thing nor can you pretend that I have. You are erroneously conflating an AVERAGE rate over time with a UNIFORM rate over time. And the more you engage in dishonest definitional changes like that, the less credible your criticism is.

But I am glad you finally admit that this is pointing to some very intriguing possibilities. If all the DNA changes occurred in a time too short for the various mechanisms currently proposed, as increasingly appears to be the case, then there must be some other mechanism at work. And isn't that much more interesting to consider than simply trying to find a way to defend an outmoded and erroneous hypothesis?


Smock Man: It is about observed vs theoretical. Torin, Vox already agreed, as do I, that your theoretical case is possible. What Vox is saying is that if every time we observe the rate of change, and it contradicts the theory, we should begin to be skeptical. The observations we see dont make the theoretical case impossible. But you need to revise your arguments if they disagree with observation. And we are seeing that, which is a good thing.


Torin McCabe: Are you one of the "dread ilk" the fabled smart people who follow Vox?  So far I am less than impressed with most of those I have talked with


Smock Man: No, I am not. I didn’t read vox until 2015.


Thomas Saint:  It does not have to be uniform. But the existence of continuous change itself starts to come into question if it is absent in recorded instances. It's a matter of probability. The longer the period extant of no observable genetic changes, either addition or subtraction, the higher the average rate of change must be within the unmeasured time-frame. Evolution is starting to look like a theory that ignores probability, when the whole theory is predicated on probability.

Evolution seems a nonsense if it magically doesn't apply to a 450 year period during which populations have exploded and environments have changed to unprecedented scale. Evolution is based on 'change' as well as 'time'. Remove change, and time actually becomes irrelevant. 450 years is still a large number of human generations. There must be evidence of replacement of genetic base-pairs. Vox has established a feasible number.

Evolutionists basically have to now argue that environmental change basically has to be apocalyptic to get a single replacement of a gene pair, or that humans and in fact all species have our final form. Is that what evolutionists are arguing? This theory is really starting to ridiculous isn't it.


Torin McCabe: Yes it is a matter of probability.  Can you do some math for me: what percentage is 450 of 12 million years?  The "magic", "unprecedented", "apocalyptic", and "ridiculous" slurs are not arguments.  450 years is a good start but based on a real understanding of probability much more data is needed to explain 12 million years.  There is no need for argument, get some good coverage and the answer is there.  Stop here dude, you are making a fool of yourself


Vox: No, he's not. But you are not merely making a fool of yourself, you are being obnoxious and are very close to getting banned. First, your appeal to big numbers biologists don't understand is irrelevant. Second, according to the current understanding of the theory, the 450 years should be seeing a higher-than-average rate of fixated mutations, not a lower-than-average rate. Third, the relevant number is 9 million years, not 12 million. And fourth, the sample years being 0.00005 of the total makes them five times more statistically relevant than the 0.00001 samples that are used to correctly predict U.S. presidential elections.
Isn't it informative how rhetorical, nasty, and completely unscientific they get the more you press them on the actual facts and figures that are necessarily involved. At this point, we can't even reasonably call evolution by natural selection a "theory" anymore, as it is more accurately described as a "low-probability hypothesis" that will almost certainly be entirely falsified within our lifetimes.


UPDATE: After Torin McCabe demanded "a retraction and an apology" I banned him from the channel. He apparently believes as long as you say "if", then it's fine to say anything you want when you describe someone else's actions. It is not and that is why he is not welcome to take part in the Darkstream discourse anymore.

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145 Comments:

Blogger My 1 millionth internet profile February 16, 2019 7:24 AM  

His response to Smock Man is an excellent gamma tell.

Blogger The Deuce February 16, 2019 7:25 AM  

VD:

The defenders of the Neo-Darwinian hypothesis are losing the scientific battle, losing badly, and you know it because you're attempting to retreat to a position of "well, it could have all happened super fast in the one area that we can't examine yet."

This whole business reminds me of medievals constructing epicycles to rescue geocentrism, but it's even more reminiscent of the way that atheists like to portray religion as retreating into narrower and narrower spaces as the march of science allegedly takes more of the territory it once held.

Blogger wreckage February 16, 2019 7:32 AM  

Shouldn't they be excited to be on the cusp of the first truly transformative leap of their theory in one hundred and freaking sixty years?

Do physicists get this defensive and weird when anticipating experimental data that could fundamentally change the model?

Blogger The Cooler February 16, 2019 7:32 AM  

low-probability hypothesis

!

I've been calling it exactly this for 12 years.

They are losing their religion.

Blogger Dave February 16, 2019 7:38 AM  

Do physicists get this defensive and weird when anticipating experimental data that could fundamentally change the model?

Yes, when they're invested in the model.


"low-probability hypothesis"

It's getting there but need better rhetoric.

Blogger wreckage February 16, 2019 7:38 AM  

In twenty years time they'll be saying "Of course, back before this advance, before we knew the probabilistic universe had purpose and direction, there was room for outmoded ideas like God to impose some order on the alleged chaos."

I greatly look forward to the total and instant reversal of everything they purport to believe, and their erasure of the Christians and Christian thought that forced them to accept the new "current science"; much as they did for the Big Bang theory.

Anonymous Anonymous February 16, 2019 7:53 AM  

@The Deuce

but it's even more reminiscent of the way that atheists like to portray religion as retreating into narrower and narrower spaces as the march of science allegedly take.

Yes, evolution is a theory of the gaps. Because SJWs are the only people who project. Darwin himself started the theory openly attacking the evidence as having gaps in it, thus openly admitting he held the theory in spite of the evidence and not because of it (ie for emotional reasons not intellectual reasons) and fervently praying that further investigation would fill the gaps with evidence that better fit his theory.

150 years later Stephen J Gould was pilloried by the Darwinist establishment for publicly noticing that the fossil record is orders of magnitude worse for Darwinism than it was in Darwin’s day.

Now the biologists are learning the same hard lesson and they don’t like it any more than the paleontologists did.

The truth can only set you free if you follow it.

Blogger Franz Lyonheart February 16, 2019 7:53 AM  

Vox, your criticism of Evolution Theory isn't even that new (although I obviously have no reason to doubt that you developed and carefully ran through your calculations yourself). "Hard" scientists in Physics, Mathematics etc. always have been rather uneasy with the statistical sloppiness of their remote cousins, the evolutionary biologists.

In his autobiographical book, Der Teil und das Ganze, the world's leading nuclear physicist Werner Heisenberg explains exactly his doubts which are VERY similar to Vox's criticism. The biologists simply don't have the extremely low probabilities implied by their unlikely theory under control.

In his book, which I'm happy to have as Hardcover edition at home, Heisenberg tells a little metaphorical story :

Two men hike up a mountain. They look across the mountain range, and spot a hut on the opposite slope. Explains one to the other : "Look over there, that hasn't always been a mountain hut. In fact, billions of years ago, there wasn't even the mountain range here. Then geological forces pushed up the rock; erosion knocked it back down; forests grew; lightning struck down the trees, and over millions and millions of years, rock and timber just fell and was randomly mixed up. On most mountain slopes, nothing of note happened. But by sheer chance, on this slope over there, the timber and glass and rock happened to fall just so, and over the millions, the pattern of a house came to be. It stood there for many hundreds of years. Then later, some people found it, and they moved in. They live there now. "

Anonymous Anonymous February 16, 2019 7:53 AM  

SJWs are NOT the only people, etc

Blogger Lazarus February 16, 2019 8:05 AM  

Around 1830 when Darwin rode the Beagle, the population of the Earth was around 1 billion. It is now approaching 7.7 B

World Population Clock

Now that humans are plentiful as bacteria, will this affect these calculations?

My canon is of middle calibre, yet I am as curious as a croissant.

Blogger Azure Amaranthine February 16, 2019 8:11 AM  

"At this point, we can't even reasonably call evolution by natural selection a "theory" anymore, as it is more accurately described as a "low-probability hypothesis" that will almost certainly be entirely falsified within our lifetimes."

Where have I heard that before. Oh right, everyone who understands the scientific method and the classifications of observation/hypothesis/theory/law.

"His response to Smock Man is an excellent gamma tell."

This: "So far I am less than impressed" no one cares.

"Shouldn't they be excited to be on the cusp of the first truly transformative leap of their theory in one hundred and freaking sixty years?"

If they clung to it for the reasons they claim, absolutely. This is just the increasing evidence that they are liars and always have been.

Blogger Mr.MantraMan February 16, 2019 8:20 AM  

Years ago I concluded it was a hypothesis not a theory per my limited understanding of Ifuckinglovescience.

Blogger Unknown February 16, 2019 8:20 AM  

So as I understand the answer is to sequence more ancient DNA. The more distant in the past little to no difference to modern DNA is found the less likely is TENS? That seems reasonable and as sequencing becomes cheaper and cheaper perfectly feasible.

I see that the oldest 'human' genome sequenced is a 430,000 year old hominid believed to be an ancestor of Neanderthals. Neanderthal DNA has also been sequenced. Ancient Homo Sapiens? The oldest modern human bones are 300,000 years old found in Morocco. Has there been any attempt to extract DNA from the teeth of ancient humans?

Blogger Andrew Brown February 16, 2019 8:49 AM  

Are they seriously stumbling on statistical analysis? That's the easiest part to understand.

Blogger Man of the Atom February 16, 2019 8:59 AM  

Most biologists and their evolutionist hill cousins are innumerate.

Blogger pyrrhus February 16, 2019 8:59 AM  

The Darwinian hypothesis of gradual evolution, never confirmed by the fossil record, has become one of the retention and ultimately fixation of adaptive bits of DNA, which is a mathematical process ruled by the gambler's equation and probability in general...Since no one has ever suggested that the laws of probability are different for different species, where did creatures like the long necked giraffe, which seemingly appeared from nowhere with thousands of differences from its short necked predecessor, come from? And why?

Blogger pyrrhus February 16, 2019 9:01 AM  

@15...Someone I know who is a career biologist told me she went into biology because she was told that math was not required.

Blogger wreckage February 16, 2019 9:06 AM  

@18 Given that biologists have to deal with probability rather than certainty all the damn time, that's... unsettling.

Blogger Robin February 16, 2019 9:15 AM  

Once Darwinism is disproven, what next? What’s the best hypothesis? Are we back to an active Creator, be that God or aliens?

I’m ignorant of the epistemological history, how big a role did Darwinism play in creating the scientistic hubris that has lead to modern atheism? By that I mean the notion that since science could explain the development of life itself in physical terms, it was therefore capable of explaining everything else in a similar way.

Blogger Snidely Whiplash February 16, 2019 9:44 AM  

It will look very strange if we find DNA that narrows all the change to a very short period of time; and then perhaps external influence could then be an interesting hypothesis.
I that a "God of the gaps" argument I see? I guess they're valid when they support the Atheist's conclusion. Whadda ya know?

Blogger Laramie Hirsch February 16, 2019 9:46 AM  

"If all the DNA changes occurred in a time too short for the various mechanisms currently proposed, as increasingly appears to be the case, then there must be some other mechanism at work. And isn't that much more interesting to consider than simply trying to find a way to defend an outmoded and erroneous hypothesis?"

Look at the open mind Vox has in this discussion, and look at the closed-minded, obstinate attitude of the other guy. The Theory of Evolution is Leftism.

Blogger Doktor Jeep February 16, 2019 10:05 AM  

This is the outcome I expected. With Vox we need a "2 week rule". If you think Vox lost a debate or has been "defeated" on something, wait two weeks and see what happens.

Blogger Bobiojimbo February 16, 2019 10:09 AM  

Thanks, Vox. This is useful.

Blogger okjoe58 February 16, 2019 10:12 AM  

This page-topic is one to keep, many thanks, Vox.

Blogger okjoe58 February 16, 2019 10:16 AM  

I've read that Darwin was a racist. I've also read that Darwin was 'anti-racist' who wanted to prove that we all came from the same source. I think Darwin was the latter

Blogger wreckage February 16, 2019 10:20 AM  

There is an additional problem in that this argument de-randomizes evolution. It increasingly appears that mutation fixation dictates that either evolution is an active process that can be "on" or "off" for a given lineage - thus how coelacanth population A could be unchanged in the time that population B has evolved limbs, lungs, several additional layers of brain function, hard shelled eggs, placenta, fur, mammaries, and space flight; or that it has some sort of non-random sense of direction working it towards certain balances of complexity and environment - and it may require that both be true.

All of a sudden we'd be looking at a "materialism of the gaps", where we struggle to find a justification for believing that anything in the universe is directionless or random.

Blogger Silent Draco February 16, 2019 10:38 AM  

Wreckage, the biologists deal with statistics, not probability. Their sample sizes may not be large enough, depending on what's studied, to generate high confidence levels for their inferences ... assuming they understand what they're doing with the null hypothesis. Large assumption.

Many of them being innumerate, they will simply enter data or take the file, and then pull the crank on Excel, R, MINITAB, whatever. The Magic Box chunks out numbers with lots of decimal places, so it must be right. Innumerate also includes easons for significant digits.

Understanding enough probability to select a useful and powerful test design takes an engineer, statistician, or ag scientist. Agriculture, because most of the STD tools and ANOVA began with Young and others applying math and reason to agriculture.

Blogger Joel and Stacey February 16, 2019 10:39 AM  

These biologists are making a good case against polling. Don't you know that there are meelions and beelions of people out there? That's why the polls don't reflect reality.

Blogger Silent Draco February 16, 2019 10:47 AM  

Wreckage, apologies for the double post, but I'm double tacked for a while.

Evolution looks more like a stochastic process, stationary in some sense, memory for key features. Expected value and variance depend on time interval and on cross correlation among variables (sexual reproduction). This is getting much clearer, but need to dive a bit more into probability and then rewrite for general understanding, including my own. TL;DR, it can be shown and described, but it'll take work to define the why and how, then figure the what's, none of which include IFLS.

Blogger Birdman February 16, 2019 10:51 AM  

@8 he already knows that

Blogger FUBARwest February 16, 2019 10:55 AM  

"Evolution looks more like a stochastic process, stationary in some sense, memory for key features. Expected value and variance depend on time interval and on cross correlation among variables (sexual reproduction). This is getting much clearer, but need to dive a bit more into probability and then rewrite for general understanding, including my own. TL;DR, it can be shown and described, but it'll take work to define the why and how, then figure the what's, none of which include IFLS."

Is it a normal part of the scientific process when faced with evidence that disproves a hypothesis to continue to adjust/alter/change said hypothesis?

Why is it so hard for some people to go "This is wrong. Time to move on to all the other possibilities."

Blogger Unknown February 16, 2019 10:56 AM  

Sub Saharan Africans have zero Neanderthal DNA, Eurasians have on average 2%. So there has been NO inter breeding between Eurasians and black Africans for at least 40,000 years. Two distinct and geographically separated populations over a prolonged time period, with the Eurasian population in particularly experiencing unprecedented environmental change with frequent bottlenecks due to natural disasters and war.

Blogger Nate February 16, 2019 11:10 AM  

They didn't go into biology because they were good at math.

Blogger Man of the Atom February 16, 2019 11:11 AM  

@31 FUBARwest
Why is it so hard for some people to go "This is wrong. Time to move on to all the other possibilities."

Pride and Rice Bowls.

Blogger occasionalcommenter February 16, 2019 11:22 AM  

Vox, have you read Michael Behe's (Of Darwin's Black Box fame) The Edge of Evolution? He also notes that time/mutation rates and number of organisms are insufficient to account for everything TENS advocates say they are, and posits the amount of accountable variation at somewhere between species and order level. Would be interested in your take on his work.

Blogger Solon February 16, 2019 11:52 AM  

I just bought and am currently reading "The Irrational Atheist" and it's funny how the current crop of biologists are looking VERY similar to the current crop of Neo-Atheists.

They will bend over backwards and jump through burning hoops blindfolded to try to show that God doesn't exist, or He's an evil tyrant responsible for all the ills of the world, and so on and so on.

Both groups have staked their entire egos on arguing against God.

It just boggles the mind. What is so hard in admitting that you were wrong? Leftism does the same thing: take a position against reality and defend it, screeching, to your dying breath, even if your castle has been built on sand and is collapsing, with you in it.

I suppose that's an apt metaphor: better a king in a crumbling castle than a peasant shivering in the cold. Outside their castle ("atheism" or "TENS"), they have no authority, no status.

Definitely looks like Leftism. Power and authority is all that matters to a Leftist, not reality or truth. I just don't understand that world view at all.

Now, there isn't enough hard evidence to show that Creationism is definitely true, but it fits the current data quite a bit better than TENS does. Maybe we do find the missing genetic link between long necked giraffes and short necked ones, but we've had 200 years to find it and haven't yet.

C'mon TENS folks: leave your castles. It's really not so bad out here with us "ignorant peasants." We won't hold it against you if you admit you were wrong, but the longer you clutch your meagre pearls, the more foolish you look.

Blogger Ron February 16, 2019 11:59 AM  

It was inevitable from the beginning. Those people who used evolution to justify their rebellion against God ended up having fewer children. The people who successfully ignored evolutionary theory had more children. Those children were necessarily selected for resistance against this miserable curse of a theory.

Eventually the only people around will be those who are genetically predisposed to regard evolution as nonsense.

Blogger tz February 16, 2019 12:13 PM  

You have a computer that cracks passwords from hashes.
It takes an average of two hours to crack a password.
Someone claims to have used it to crack a million different passwords. You point out that it would take over a thousand years.
They turn around and say "but it is using the 3d graphics card! haha, I've defeated your argument".

Evolution as a replacement for design or engineering is basically an anti-entropy machine (in both the thermodynamic and Claude Shannon Information Theory sense).

Every debate comes down to the observation that there is a lot of measurable negative entropy involved (the height of the tree), over the time allowed (the number of rings).

Even the original ones with Paisley and Lord Kelvin - and I'm not even sure about the alleged "age of the earth". Engineers, or even blue collars in ISO-9000 factories have to measure error. I can't get straight answers as to "plus or minus what percent?", and they multiply assumptions until 4.5 billion years really means anywhere from 100,000 to 50 billion. Maybe I'm exaggerating, but I'd like someone unbiased to take all the data and do the calculation.

You see this in miniature - was the common ancestor 4m, 9m, or 12m years ago?

Then they fudge - mutation rates fast, fixation is also fast or not? Sometimes the wolves get the fittest sheep before it can breed just out of chance.

So first the time is made as long as possible, and the fixation rate as fast as possible, except the numbers don't correspond to what we would expect to see.

Every scientific advancement pushes this farther apart. Darwin imagined a feedback system that could create men who could live on air in the arctic in 100k years as long as the stresses were gradual.

But then we figured out DNA, and worse, that it is very small and conservative, so stresses are more likely to create extinction.

Blogger tz February 16, 2019 12:26 PM  

As part of the ledgerdemain (double book entry keeping), they change the number or make it irrelevant. Example is the number of mutations between a human parent and child.

1. Is that mutations that don't change the amino acid they code for? Technically they are mutations, but there is no change in the microphenotype.

2. Even if it changes one amino acid, if it isn't in the critical area or doesn't change the function, is that a mutation, like a screwdriver with an orange instead of yellow handle.

3. If it does matter it is most often hurtful or deadly - the genes that cause colorblindness, hemophelia, don't have a backup in men, and there are others that were deadly (diabetes, phenylketonuria). Or simple too much of the right thing in all the trisomy problems. I know of only one example of a positive mutation, and that is sickle cell trait, which apparently resists malaria, but kills when you get two and sickle cell anemia.

So bad things are apparently fixed at a rate faster than anything good. The bad things happen more frequently because more entropy happens much more frequently than negative entropy.

As an example where evolution should have been helpful was the Irish potato famine. There were millions of potato plants. None developed resistance to the fungus. Eventually a copper based anti-fungal was found. What is the mutation/fixation rate?

Blogger KPKinSunnyPhiladelphia February 16, 2019 12:28 PM  

FUBARwest wrote:"Evolution looks more like a stochastic process, stationary in some sense, memory for key features. Expected value and variance depend on time interval and on cross correlation among variables (sexual reproduction). This is getting much clearer, but need to dive a bit more into probability and then rewrite for general understanding, including my own. TL;DR, it can be shown and described, but it'll take work to define the why and how, then figure the what's, none of which include IFLS."

Is it a normal part of the scientific process when faced with evidence that disproves a hypothesis to continue to adjust/alter/change said hypothesis?

Why is it so hard for some people to go "This is wrong. Time to move on to all the other possibilities."


Why should evolution -- or better yet the process of speciation or species change-- be constant? There are ancient life forms, and there are newer life forms.

Blogger Torin February 16, 2019 12:32 PM  

Copy paste for YT:

Yes Vox we are agreeing on what data is required and the limitation of the model. Now we can see if you are a honest and good man and one who quickly admits that you are wrong like you said in this stream. I want a retraction and apology for you saying I am lying ("you tell ridiculous lies") and engaging in "dishonest definitional changes". I clearly said "*IF* you assume that the rate of change is uniform across time" and then clarified the problems with that assumption; an assumption that many in this thread did not understand. Pointing out the unstated limits of models and how to overcome is not "erroneously conflating"; rather it helps increase understanding and is the reverse of dishonest. If you want to play rhetoric for fun or to impress the low IQ then you can slime me as "attempting to protect evolution" but not that I am telling "ridiculous lies"


>> It doesn't help when you tell ridiculous lies like: "again you are jumping gun if you assume that the rate of change is uniform across time". I have never, ever assumed any such thing nor can you pretend that I have. You are erroneously conflating an AVERAGE rate over time with a UNIFORM rate over time. And the more you engage in dishonest definitional changes like that, the less credible your criticism is.

Blogger Mr.MantraMan February 16, 2019 12:36 PM  

"After Darwinism?" well how's about Galtonism?

Blogger FUBARwest February 16, 2019 12:41 PM  

"Why should evolution -- or better yet the process of speciation or species change-- be constant? There are ancient life forms, and there are newer life forms."

I did not say it needed to be constant. I asked why people feel the need to defend a hypothesis that looks increasingly improbable.

Blogger tz February 16, 2019 12:42 PM  

Except for the few Young Earth Creationists, most Christians would not be bothered by evolution, but see it as just another wondrous natural law given by the creator, like the laws of physics.

But Christians really want to know WHAT IS TRUE. And most know how to use reason, evidence, and mathematics to determine it.

Atheists have an irrational need for there to be no God (and hence no Devil). So they need Evolution or some similar amoral, mindless mechanism to have resulted in their existence. And they won't let that go any more than the flat-earthers and dismiss and deflect every reasonable objection, the more clear and irrefutable, the more it is like a crucifix to a vampire (or demon!).

The other place you see this is in morality. Molyneux is the only Atheist that is trying to reintegrate sexual morality into the system, but hasn't revised UPB.

Individuals just need to consent, even if collectively it destroys civilization.

Atheists do have problems with murder and theft, but not any form of sex (children are more "yuck" than calling it evil - ask them why should it be a "sin"). Also why few object to abortion - but can't define when the baby is a person coherently.

This is clear to anyone looking at it. Atheism is a cult even if of individuality. No responsibility.

And assume we find a mechanism that adds direction to the mutation and fixation. What happens to the Atheists if it means that women - by the rules of the mechanism - should marry young and have children, not college and careers? That men and women's different bell curves are predicted?

The other big contradiction is if you ask any Evolutionist about the logical Eugenic implications. Margaret Sanger and the Nazis were right? Racial, or at least Human genetic hygeine? Kill the useless eaters? Darwin created Eugenics.

On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life

I'm not a racist or supremacist, I'm a Darwinist and wish to preserve my favored races!

Blogger tz February 16, 2019 12:46 PM  

@41 - so there is no mechanism or evidence that the fixation rate has an accellerator or a brake, but you can assume it changes so it is really fast when you need it to be but can see it, but slows to a crawl when we try to measure it today.

If you are proposing a theory of variability, it should be robust and testable (and the book Evolution 2.0 suggests such), but when you say "oh, the rate is just an average", it becomes an epicycle instead of a theory.

Blogger Unknown February 16, 2019 12:54 PM  

@39- neither the sickle cell trait or the white skin mutation, in Northern Europeans and North East Asians, has become a fixed genetic mutation in our species. In fact both of them may well end up being a genetic dead end despite being enormously beneficial to the populations they express themselves in. Protection against Malaria and being able to absorb vastly more Vitamin D from sunlight when ingesting a diet low in meat and fish (which currently is most of the human population). What's not to like?

Blogger KPKinSunnyPhiladelphia February 16, 2019 12:55 PM  

VD spoke:

The Neo-Darwinian hypothesis has not been conclusively falsified, not yet, but the probability that it will be is rapidly increasing with advancements in genetic science. And with every retreat to "yeah, but I can imagine that this thing we haven't ever observed is still theoretically possible", more and more people are rhetorically convinced that the Darwinian emperor has no clothes.

Well, I guess we'll see.

The advances in whole genome sequencing are nothing short of remarkable, and we are beginning to see just a few of robust inferences we can draw, not only about population genetics but also about epigenetic activities that make "lifeless DNA" spring to action.

And, since we are all concerned here about the math, one of the key inferences drawn is the scale of modern human development. The sophisticated applied mathematical techniques applied that allow reasearchers to "work backwards" to different time points in genetic development certainly put the lie to any claim about extremely short time cycles for, say, spontaneous acts of sub species differentiation or single species lineages.

I urge everyone who is interested in this topic read David Reich's book, "Who we Are and How We Got Here."

Anonymous Anonymous February 16, 2019 12:59 PM  

"Leftism does the same thing:"

Atheism is the foundation of leftism. You have to kill God before you can decide what is good and what is evil for yourself.

Blogger Irish Energy February 16, 2019 1:05 PM  

Dawkins says there is no such thing as the missing link, that the progressions were too slow and unnoticeable for a missing link fossil to be found. So if the Darwin defenders are now saying the change could have happened in a short period of time ,then that implies there should be a missing link fossil out there waiting to be found .

Anonymous Anonymous February 16, 2019 1:09 PM  

"Except for the few Young Earth Creationists, most Christians"

"For strait is the gate, and narrow is the way, that leads to salvation, and few there be that find it."
--some guy.

Resort to popularity is not an argument.

But I like to ask the theistic evolutionists a simple question:

What's the different between theistic evolution and atheistic evolution?

Hmm?

Blogger FUBARwest February 16, 2019 1:19 PM  

"What's the different between theistic evolution and atheistic evolution?"

*If* the theory was true, is there a reason the process of evolution couldn't be the *how* God created the species?

Anonymous Anonymous February 16, 2019 1:30 PM  

1. God says he cannot lie.
2. God says that death came into the world by Adam's sin.
3. Theistic evolution says God "created" (even using that term is highly dubious*, it would be more accurate to use "developed") man using billions of years of death, decay, predation, sickness, etc.

You do the math.

*The Chaldean/Hebrew is emphatic and clear; it is not talking about building a house out of existing materials kind of activity, but the making of something from nothing. "ex nihilo" as it is known in the Latin.

There's very strong reason why the God described in the Bible could not be the author of a process like evolution. If, otoh, you prefer some alien benefactor, well that's your prerogative.

But then you are just kicking the can down the road; where'd the alien come from? You either end up back with the eternal steady state universe model (discarded in favour of the big bang), or you end up with a singular uncaused event beyond which no explanation is possible.

Take your pick.

Anonymous Anonymous February 16, 2019 1:32 PM  

But you haven't answered the question:

What's the difference?

Blogger Dire Badger February 16, 2019 1:35 PM  

Resident Moron™ wrote:

What's the different between theistic evolution and atheistic evolution?


The same difference between Monet and Jackson Pollock.

Blogger FUBARwest February 16, 2019 1:40 PM  

"God says that death came into the world by Adam's sin."

Can something "die" that does not have a soul? I.e. a cpu for example?

"The Chaldean/Hebrew is emphatic and clear; it is not talking about building a house out of existing materials kind of activity, but the making of something from nothing. "ex nihilo" as it is known in the Latin."

Could you link something to this? I'm interested in learning more.

*If* the process of evolution was used it would have started "ex nihlo". Is there something in the text that prescribes a time limit?

For the record, especially after Vox's foray into the topic, I don't believe evolution is a viable explanation for life on Earth. Even before the argument presented on this blog I felt the probability it happened at random was so low you'd have to be retarded to think an outside force wasn't involved. I've never understood the Christian opposition to the theory. I don't understand how it is inherently contradictory.

Blogger WillBest February 16, 2019 1:43 PM  

The Samples for Presidential elections attempt to be stratified and random. Sampling the last 450 years is neither stratified nor random. I would also note that neither are the bones that we are fortuitous enough to happen across since the conditions for preserving something hundreds of thousands to millions of years are not going to create a random sample either.

Evolution doesn't make any particular sense from a logic standpoint because it requires you to fight against entropy. It is more likely that life started as a a higher order gene code and has been degrading ever since than other way around. But then that raises the uncomfortable question for atheists as to where that came from.

Just look at Down Syndrome. Its not a random mutation since it keeps appearing. Which means the conditions for it must have been set generations ago otherwise it wouldn't happen enough for anybody to identify it. If they were more functional however they would ultimately be a less order human offshoot. And failed off shoots are going to occur with far greater frequency than enhanced ones.

Blogger FUBARwest February 16, 2019 1:43 PM  

"What's the difference?"

Atheistic claims it is random. Theistic claims it is the mechanism God used to create life.

Anonymous Anonymous February 16, 2019 1:53 PM  

"Could you link something to this? I'm interested in learning more."

My best advice is to get a good concordance (Strong's is good) and study it for yourself.

The Bible (or God, if you believe it is the word of God) doesn't say that man HAS a soul, nor does it say that God GAVE man a soul.

It says that man IS a soul. (Genesis 2: 7 "And the Lord God formed man of the dust of the ground, and breathed into his nostrils the breath of life; and man became a living soul.")

Again, the word translated as "soul" means either breath or spirit, depending on the context. But that word is also used when he Bible says that "God IS a spirit".

In contrast it say of man that "He IS flesh". The Bible is a book of contrasts; we're not the same as God. We do not share either his nature (we#re not made of the same"stuff" nor do we share his character).

And regarding the meaning of the word soul, we used to know this. We made the code SOS (Save Our Souls) not as a plea to pray that the ghosty part of me goes to the right place when my body dies, but as a plea to come and save my life.

The biblical term soul is used to refer to the whole person, everything about them; it is the opposite idea to the dualist notion of flesh vs ghost/spirit. You see this in a number of examples where the Hebrew "repetition for emphasis" pattern describes things like:

"with all thine heart, and with all thy soul, and with all thy might."

It means "with everything you are".

Blogger FUBARwest February 16, 2019 2:04 PM  

Thanks @Resident Moron. I'll take your advice.

"Genesis 2: 7 "And the Lord God formed man of the dust of the ground, and breathed into his nostrils the breath of life; and man became a living soul.""

Is there a reason to believe that those actions happened immediately in sequential order? What is contradictory in those actions happening over "x" amount of years?

"Again, the word translated as "soul" means either breath or spirit, depending on the context. But that word is also used when he Bible says that "God IS a spirit".

In contrast it say of man that "He IS flesh". The Bible is a book of contrasts; we're not the same as God. We do not share either his nature (we#re not made of the same"stuff" nor do we share his character)."

Why doesn't that support the idea that "Man" as an animal was created without a "soul" and then given one at a certain point in time?

"with all thine heart, and with all thy soul, and with all thy might."

I do not know any Hebrew besides Yahweh, or the grammatical/semantic rules of Hebrew but is there a reason the use of three different words would be used to convey the same meaning? Reading that with my current understanding leads me to believe those each mean seperate things. Perhaps this will be cleared up with further study on my part.

Anonymous Anonymous February 16, 2019 2:07 PM  

Atheistic claims it is random. Theistic claims it is the random mechanism God used to create life.

FTFY.

There is no difference. The TE's are even more rabid in their defenses of darwinian evolution than the atheists (because their whole self-image depends on it).

If only they were half as keen on defending the word of God.

Blogger FUBARwest February 16, 2019 2:15 PM  

"Theistic claims it is the random mechanism God used to create life."

It can't be random if God planned it out. That doesn't fix my statement. But what's wrong with that position?

Anonymous Anonymous February 16, 2019 2:27 PM  

"Is there a reason to believe that those actions happened immediately in sequential order? What is contradictory in those actions happening over "x" amount of years? "

That's beside the point. the point is the meaning of "soul". The soul is what man BECOMES when the flesh is made alive by the breathing in of the spirit of life.

It is not what he possesses, it is what he IS.

Regarding the quoted phrase ("with all thine heart, and with all thy soul, and with all thy might") there are two major objections to this being a list of different things:

1. The Hebrew literary practice of repetition is well-known and VERY common in scripture. We can't pretend it doesn't exist just to favour a particular interpretation.

2. If we turn all those repetitions into lists of different things we really mess with the sense of the whole book, in some cases giving absurd results.

But the fact is that we do know, and have done for many centuries, that the Hebrew writers used repetition for emphasis, e.g. "Babylon is fallen, is fallen ... "

Finally, since I became a Christian I've been of the view that those of us who call ourselves by his name ought to pay respect to what he actually said. he treated the books of Moses as utterly authoritative and quoted them as real history. He quotes Adam's creation in support of his arguments about marriage and divorce, for example. Moses wrote that God made the heavens and the earth and in the same week he made man. That leaves even less time for evolution than Vox.

And Christ says this, which ought to give us pause:

"If they believe not Moses and the prophets, they will not believe though one be raised from the dead."

Jonathon Sarfati has two very comprehensive books on evolution:
- Refuting Evolution
- Refuting Evolution 2

His "The Genesis Account" is also very good.

You can get them from Amazon. IIRC, one of them does a pretty good job of refuting the "long ages in Genesis creation week" argument often resorted to by theistic evolutionists.

J O Moreland, Stephen Meyer, Christopher Shaw, Ann R Gauger, and Wayne Grudem produced a massive tome called "Theistic Evolution" which thoroughly refutes both kinds.

But be warned, it really is massive. And expensive.

Anonymous Anonymous February 16, 2019 2:33 PM  

The fundamental issue is TIME.

The deep time of modern atheistic cosmology was utterly required to allow darwinism to be even remotely plausible. But there's no good reason to believe it. There's no good reason to let the unbelievers define the fundamental nature of reality for you.

The issue every Christian faces today is the exact same issue faced by Adam and Eve:

Who you gonna believe?

The beauty is, you get to choose for yourself.

Anonymous Anonymous February 16, 2019 2:34 PM  

But what's wrong with that position?

You mean apart from making God a liar?

Blogger chronoblip February 16, 2019 2:41 PM  

Resident Moron™ wrote:2. God says that death came into the world by Adam's sin.

Romans 5:12 doesn't say that:

Therefore, just as through one man sin entered the world, and death through sin, and thus death spread to all men, because all sinned—

The "death" referred to by Paul is not physical.

Therefore, as through one man’s offense judgment came to all men, resulting in condemnation, even so through one Man’s righteous act the free gift came to all men, resulting in justification of life. For as by one man’s disobedience many were made sinners, so also by one Man’s obedience many will be made righteous. - Romans 5:18-19

For the wages of sin is death, but the gift of God is eternal life in Christ Jesus our Lord. - Romans 6:23

but has now been revealed by the appearing of our Savior Jesus Christ, who has abolished death and brought life and immortality to light through the gospel, - 2 Timothy 1:10


The death that Jesus abolished was not physical, as every Christian since Christ has still eventually physically died.

If the death that Jesus abolished wasn't physical, on what scriptural basis are any required to believe that the penance for sin as described by Paul was a physical death as well, let alone that death in all the physical world is a result of Adam and Eve's sin?

Then the Lord God said, “Behold, the man has become like one of Us, to know good and evil. And now, lest he put out his hand and take also of the tree of life, and eat, and live forever”— therefore the Lord God sent him out of the garden of Eden to till the ground from which he was taken. - Genesis 3:22-23

And I'll even do you one better. Is deception ever a sin?

But I fear, lest somehow, as the serpent deceived Eve by his craftiness, so your minds may be corrupted from the simplicity that is in Christ. - 2 Corinthians 11:3

To assert that Adam and Eve are the ones who brought sin into the physical world would also require asserting that the serpent did nothing wrong, because what the serpent did occurred prior to Adam and Eve having taken of the fruit.

Had Adam and Eve been obedient, there was still sin in "the world", and so even if you persist in the assertion that the consequence of sin is a physical death, we'd still have sin, and physical death, before The Fall.

Your move.

Blogger Servant February 16, 2019 2:48 PM  

What's wrong is that's not how God said he did it

Blogger Servant February 16, 2019 2:52 PM  

Sorry for double post but i have to point out that chronoblip doesn't know how to read

Blogger FUBARwest February 16, 2019 2:59 PM  

"That's beside the point. the point is the meaning of "soul". The soul is what man BECOMES when the flesh is made alive by the breathing in of the spirit of life.

It is not what he possesses, it is what he IS."

How can man become "soul" when you previously said "man is flesh"? I thought that was the reason God sent his only son. The idea that God became Man to save Men. How can that be if Man is Soul and God is already Soul? I don't think it is beside the point at all. I dont see why the animal of man could have been created via evolution then God breathed life into him and gave him a soul. As already stated, TENS via natural selection is so improbable imo that you have to place unfounded faith into it, but I still don't see the Christian animosity towards it.

"But the fact is that we do know, and have done for many centuries, that the Hebrew writers used repetition for emphasis, e.g. "Babylon is fallen, is fallen ... ""

That doesn't clear things up for me. You just used an example where the repetition used the same word. I recognize 100% that repetition is used to emphasize things. It is not repetition when you use different words.

"Moses wrote that God made the heavens and the earth and in the same week he made man."

"The fundamental issue is TIME."

I agree 100% the fundamental issue is time. What I'm confused about is why do we assume time is the same for us as God.

Anonymous Anonymous February 16, 2019 2:59 PM  

"The "death" referred to by Paul is not physical."

Paul doesn't say that. Where did you get it from?

Adam and Eve were given dominion over the earth. In choosing to follow Lucifer they ceded that dominion, which bought the whole earth under his influence and under the curse of sin.

Sin existed before their sin, and was "in the world" but confined to the tree of knowledge of good and evil. Its effects, most particularly in this context, death, came "into the world" through Adam's sin, not Lucifer's. He had no dominion here so his condition was irrelevant until Adam fell.

The life we are promised is physical. It says we will build houses and live in them, plant vineyards and eat of the fruit of them.

And by what rule of exegesis do you make this division? Do you apply this principle consistently, or only to defend a position not stated in the word itself?

The word says; "the SOUL that sinneth, it shall die."

In which case, the division you're defending so ardently is irrelevant. What happens when the soul dies, in your understanding?

"the simplicity that is in Christ"

I believe what Christ said.
I believe what God said.
I believe God speaks every human language well enough to speak plainly, and did so.
I believe God is able to preserve the plain meaning of his word, and did so.

(We know without doubt that ancient Chaldean and Hebrew had distinct words for the concepts of building, causing, and creating. There's no ambiguity at all in the language, that it is intended to be a literal historical account.)

Blogger FUBARwest February 16, 2019 3:03 PM  

"We know without doubt that ancient Chaldean and Hebrew had distinct words for the concepts of building, causing, and creating. There's no ambiguity at all in the language, that it is intended to be a literal historical account.)"

It sounds like my confusion will be cleared up when I learn/find out the Hebrew meaning of the words in the bible.

Blogger Daniel Babylon February 16, 2019 3:04 PM  

Since older DNA has all decayed couldn't evolutionists permanently retreat into the argument that "there was a time of superfast mutation?"

Blogger VD February 16, 2019 3:12 PM  

Dear would-be theologians,

Shut the fuck up already. You're totally off-topic and this is precisely why no one pays any attention to anything you say. Want to know why I despise theologians? This is why.

Love,
Everyone capable of staying on topic

Blogger gecko February 16, 2019 3:16 PM  

The mathematical argument identified by Vox is sound, but Darwin himself identified the criteria for falsification using a much simpler mathematical argument that is likely easier for most people to understand:

If TENS posits that unsuccessful mutations outnumber sucessful ones by many orders of magnitude, then the probability that *any* fully-formed fossils would be found is extremely remote. That is, the *only* fossils we should expect to find would be the evolutionary discards, mutant beasts with species-terminating defects. In reality, the fossil record shows exactly the inverse of that.

Blogger Ceasar February 16, 2019 3:29 PM  

My theory is that Evolutionists have "evolved" into lazy asses who do not want to put in the work to perfect their "Theory".

Blogger Difster February 16, 2019 4:05 PM  

If McCabe doesn't even know who the Dread Ilk are, how does he know he's talked to any of us to determine whether he should be impressed or not?

Blogger Nate February 16, 2019 4:09 PM  

"Shut the fuck up already. "

PREACH PREACHER.

Anonymous Anonymous February 16, 2019 4:21 PM  

Sorry Vox, all.

my fault, got carried away. Should I delete?

Blogger VD February 16, 2019 4:27 PM  

Did I tell you to delete it? No.

What did I tell you to do? Do that.

Blogger chronoblip February 16, 2019 4:41 PM  

I am sorry for having posted in such a boorish manner. It was very inconsiderate for me to behave in such a way as your guest.

Blogger Nate February 16, 2019 4:51 PM  

Darwinism is a Religion... and as you expose it as false... and ask questions they cannot answer... they are going to get more and more nasty.

Blogger Aaron B. February 16, 2019 5:08 PM  

I know a kid who enjoys science but is bad at math, like struggles-with-fractions-bad. Guess what he's majoring in.

Blogger tz February 16, 2019 6:31 PM  

The theological discussions have been hashed before ad nauseum. But they show the identical problem is some just won't give things up, either when there is a root disagreement that isn't resolvable by experiment or evidence, or that when it is refuted by reason, experiment, and evidence, there is a retreat to "there must be something wrong with them, or some other unknown variable that would make my belief true".

I was skeptical of Evolution when growing up because I already knew what actual science was, and Evolution was at best a mythology to explain things without direct divine intervention. And it was something Scalzi might write.

Also back then we had connect the (numbered) dots books, so you would start at 1 and when finished, you would trace out an elephant. You just needed to know what N+1 was and draw straight lines. TENS proponents somehow don't hit some dots, do others in the wrong order, draw angles, end up with a donkey instead, and insist that is what was supposed to be drawn in the first place.

Way back then Evolution was dubious. Today it has effectively been falsified on many levels by many methods, based on basic mathematics, statistics, physics, and chemistry. Giving a huge benefit of the doubt, the additional evidence is 20% pro Evolution (in any form), but 80% anti. The additional information is grabbed as "this is how it might have happened", but then shows it would be even more difficult to happen without some design, engineering, etc.

Finally, we have AI, SuperComputers, and the Internet. Yet there are ZERO things I know of that are trying to develop applications or find answers by random mutation, and silicon could do teramutations per second, and gigamutation fixes per second. There have been "interesting" mutagenic models, but they don't really prove anything.

We can't even make TENS work in a minimal and 10 orders of magnitude faster simulation using computers today.

(I'm also enjoying the lack of talking about "primordial soup", beyond the environment that would destroy life, it doesn't produce the RNA parts for primordial replication, and RNA is more fragile than protein.).

Blogger tz February 16, 2019 6:32 PM  

Vox, you have to admit that Bubbles and Michael Jackson didn't diverge as much as is alleged by the TENS advocates.

Blogger tz February 16, 2019 6:38 PM  

Apparently JF is a Neurobiologist. Someone needs to ask him when the unborn baby starts to feel pain.

Blogger Bilroy February 16, 2019 9:25 PM  

How's this for rhetoric to show how tardy a selection process natural selection would be:

How many people do you know with very long limbs actually go on to become boxers?

Blogger David F February 17, 2019 2:25 AM  

This is all ridiculous. I'm surprised you're dealing with third-raters who can't do the math.

Find someone who can, and it's obvious there's no need for acceleration, no need for anything but the rate of mutation we presently see in humans.

30 mutations per offspring = 30 fixations per generation.
450,000 generations * 30 = 12.5 million fixations.

Nothing else is needed.

Blogger Azure Amaranthine February 17, 2019 4:31 AM  

"Find someone who can, and it's obvious there's no need for acceleration, no need for anything but the rate of mutation we presently see in humans."

How many times does it need to be pointed out to you that mutation rate is irrelevant so long as it passes a certain much lower threshold?

Blogger notjoshing February 17, 2019 4:44 AM  

It is hard to fix a mutation across a large population. Evolutionists counter this problem with the suggestion that a mutation can be fixed in a small subset of the population, which then replaces the rest of the population. Basically, they liked to read a lot of Chris Claremont X-Men.

Blogger wreckage February 17, 2019 4:46 AM  

@86, I disagree with many things Vox says and concludes, but in my limited experience, if you think he's made a basic error, it's because you misread him badly. Go back and try again. The issue in question is the number of mutations per generation that displace their informational precursor across the entire population, NOT the raw number of errors per generation.

Blogger notjoshing February 17, 2019 4:55 AM  

Evolutionists have been aware of the problem of fixing dramatic changes for a long time. George Gaylord Simpson, the father of epicycle evolution, conceived of quantum evolution long before Gould absconded away with the idea. The concept was that genes did not need to be fixed in a large population, only a small one, and that the new population then replaces the original. This early attempt to save TENS suffers from exactly the weaknesses Vox is pointing out.

Blogger notjoshing February 17, 2019 5:03 AM  

For "living fossils", we cannot say they have not been evolving; all we have is the phenotype to look at, and compare to fossils. Biochemically, we have no idea how similar or different the coelacanth is to those precursors found in the fossil record. Sequence comparisons suggest they are not unchanged. If that makes you wonder, "What good is the fossil record for proving or disproving TENS?", then you're asking a good question.

Blogger notjoshing February 17, 2019 5:10 AM  

Science requires proof. Just so stories make for good stories, and poor science

Blogger notjoshing February 17, 2019 5:20 AM  

Scientists regularly generate antibiotic populations of bacteria in the lab. The process largely consists of selecting who lives and who dies, allowing (or encouraging or introducing) variations to occur from which to select. This is a common model for Christian evolutionists, with God introducing variability and selecting populations, e.g. Adam and Eve. The secular model assumes randomness and self-organization takes care of all this.

Blogger notjoshing February 17, 2019 5:26 AM  

God says he did it, not the process used to do it. If he said how to create life, Urey and his ideological descendants would have been out of business long ago.

Blogger VD February 17, 2019 5:46 AM  

This is all ridiculous. I'm surprised you're dealing with third-raters who can't do the math. Find someone who can, and it's obvious there's no need for acceleration, no need for anything but the rate of mutation we presently see in humans.

You're a fourth-rater who doesn't even understand the underlying issue. And here I am dealing with you. This is the part that is completely wrong: 30 mutations per offspring = 30 fixations per generation..

Blogger carry_bit February 17, 2019 11:34 AM  

David Fenger wrote:30 mutations per offspring = 30 fixations per generation.
I'm currently performing some experiments on a toy simulation I'm writing, in part to see if that is the case.

Some interesting things I've observed so far:

* It's not exactly equal, but not too far off either. 1 mutation per individual results in about 0.73 fixed mutations accumulating per generation; 4 mutations result in about 3.08
* The cumulative fixation rate does not change much over time (there are no large accelerations)
* Previously fixed mutations are removed from the population at a steady pace too, at a rate that doesn't change much over time
* The size of the genome has little effect on the cumulative fixation rate
* Mutation rate has little effect on the average time it takes a single mutation to fixate
* As a result of the above, effective parallelism decreases with increase mutation rates
* Causing a disaster that bottlenecks the population and changes which traits are favored does surprisingly little for fixation

Blogger David F February 18, 2019 12:03 AM  

@96 Interesting, I'm seeing around .9 to .95 of the mutation rate in my sim. Part of that is gene saturation - I've got a binary gene model that only mutates from 0 to 1, to make it easier to count mutations. So after enough mutations build up, the effective mutation rate starts to fall.

Another thing to be careful of is that starting the sim from 0 mutations is going to skew your numbers. You want to give it enough time to hit something close to steady state before calculating the rate. Calculating the rate of the second half of the run produces more accurate results.

At larger timescales the fixation rate wasn't too bursty, but I found that at short time scales it could be - many generations with none, then suddenly a batch all at once when a line dies out.

Not sure what you're seeing about "effective parallelism", though.

Blogger David F February 18, 2019 12:16 AM  

@95 VD wrote:This is the part that is completely wrong: 30 mutations per offspring = 30 fixations per generation.

I'll grant that it's more "approximately equal, in the long run" rather than strict equality. But the standard math for fixation rates is exactly that: for neutral mutations, (u * Ne) * (1 / Ne) = u

Here's the source code for my simulation: https://pastebin.com/cgBRwyMc

It shows the above from first principles - a genome only one order of magnitude short of the bacteria you reference, variable population sizes and negative mutation rates. Vary the mutation rate, and the fixation rate varies in relatively tight agreement.

There's an alternate line of argument that doesn't depend on the above as strongly: your calculation for fixation rate in humans assumes that the fixation rate is independent of the mutation rate.

The mutation rate in humans per generation is about 100,000 times higher than in the bacteria in question. (1000 from the size of the genome, 100 from replications per generation. The error rate per base pair per replication is very similar in both.)

Blogger David F February 18, 2019 12:40 AM  

@87 Azure Amaranthine wrote:How many times does it need to be pointed out to you that mutation rate is irrelevant so long as it passes a certain much lower threshold?

What exactly is the threshold? Show me the math.

Blogger Azure Amaranthine February 18, 2019 9:38 AM  

"What exactly is the threshold? Show me the math."

That's not how burden of proof works. You have to prove it first, and sims built on materialist-naturalist religion don't count, because they prove nothing. This is why we keep saying observation only, because we know you guys like to beg the question with regard to everything being according to your faith in the first place. You've got over a century of history of it.

Blogger Azure Amaranthine February 18, 2019 9:41 AM  

You can simulate until your eyes bleed. All it means is that you made yet more models preconsistent with your baseless beliefs about how the world works.

Blogger Unbiasedmike February 18, 2019 1:00 PM  

Can someone please direct me to the full exchange that Vox clipped for the blog? I've been searching for it and can't seem to find it but would love to read the whole thing. Thank you!

Blogger Ryu238 February 18, 2019 1:49 PM  

"fter Torin McCabe demanded "a retraction and an apology" I banned him from the channel. He apparently believes as long as you say "if", then it's fine to say anything you want when you describe someone else's actions. It is not and that is why he is not welcome to take part in the Darkstream discourse anymore." What?

"Vox: We can and it increasingly looks like we will. The defenders of the Neo-Darwinian hypothesis are losing the scientific battle, losing badly, and you know it because you're attempting to retreat to a position of "well, it could have all happened super fast in the one area that we can't examine yet." " So you make a claim on an assumption, and dont give evidence.

"The Neo-Darwinian hypothesis has not been conclusively falsified, not yet, but the probability that it will be is rapidly increasing with advancements in genetic science. " Really?
"You are erroneously conflating an AVERAGE rate over time with a UNIFORM rate over time." Really? But then you go,

"But the existence of continuous change itself starts to come into question if it is absent in recorded instances. It's a matter of probability. The longer the period extant of no observable genetic changes, either addition or subtraction, the higher the average rate of change must be within the unmeasured time-frame." How would we show this to your satisfaction then?
"Evolution seems a nonsense if it magically doesn't apply to a 450 year period during which populations have exploded and environments have changed to unprecedented scale" Actually if the changes to the environment ar so rapid then there wouldnt have been enough time for any fixed mutations, let alone with such a massive population boom.

Blogger Ryu238 February 18, 2019 1:51 PM  

"Second, according to the current understanding of the theory, the 450 years should be seeing a higher-than-average rate of fixated mutations, not a lower-than-average rate." Why? http://www.sciencemeetsreligion.org/evolution/dna.php

Blogger Ryu238 February 18, 2019 1:52 PM  

"Third, the relevant number is 9 million years, not 12 million." Why?

Blogger Ryu238 February 18, 2019 1:53 PM  

"beneficial mutations fixate faster among growing populations and b) the environmental changes have been greater over the last 450 years than at any time previous, including catastrophes and Ice Ages." Have you heard of neutral mutations vox? They happen more often: https://www.nature.com/scitable/topicpage/neutral-theory-the-null-hypothesis-of-molecular-839

Blogger David F February 18, 2019 2:02 PM  

@100 I have given the math multiple times: (u * Ne) * (1 / Ne) = u.

That is the standard equation for the fixation rate of neutral mutations. It is derivable from two observations:
* Neutral mutations exist
* Organisms with neutral mutations have the same survival rate as those without (or with different ones).

The rest is math, and simple math at that.

Blogger KPKinSunnyPhiladelphia February 18, 2019 4:50 PM  

Azure Amaranthine wrote:"What exactly is the threshold? Show me the math."

That's not how burden of proof works. You have to prove it first, and sims built on materialist-naturalist religion don't count, because they prove nothing. This is why we keep saying observation only, because we know you guys like to beg the question with regard to everything being according to your faith in the first place. You've got over a century of history of it.


and

Azure Amaranthine wrote:You can simulate until your eyes bleed. All it means is that you made yet more models preconsistent with your baseless beliefs about how the world works.

By those criteria, you would have to shut down every population genetics lab on the planet.

But we sholdn't worry, because they never going to be shut down, and in fact are coming up with, and will continue to come up with, robust inferences.

Because you see, the principle is simple. If you have an ancient genome, and a modern genome, you can deduce quite powerfully how much of the ancient genome, if any, passed to the modern version.

It's math. Applied math. And it's right.

Blogger Azure Amaranthine February 18, 2019 6:29 PM  

"By those criteria, you would have to shut down every population genetics lab on the planet."

If that's all they're contingent on, that's a feature.

"It's math. Applied math. And it's right."

It is not applied in the slightest.

If it contradicts observed reality it is also wrong.

If it is based on extra-scientific philosophy it is also irrelevant.

"That is the standard equation for the fixation rate of neutral mutations. It is derivable from two observations:"

And it violates other observations, so clearly there's something wrong with it.

Blogger Azure Amaranthine February 18, 2019 6:32 PM  

Namely that it's derived from two observations and an assumption.

Blogger David F February 18, 2019 10:09 PM  

@109 Azure Amaranthine wrote:And it violates other observations, so clearly there's something wrong with it.

Show me the observations that it disagrees with, please. Be as specific as possible, because I'd like to read and analyze them for myself.

Blogger Azure Amaranthine February 18, 2019 11:24 PM  

"Show me the observations that it disagrees with, please."

You're already perfectly aware, considering your presence only exists in this thread in an irrelevant attempt to rebut the product of some of them.

So, more? No.

You're still trying to play the same simulation vs observation game as in the Maximum Mutations thread, and you'll never succeed with that tactic. Again, your best hope is to validate Yockey's guess about Vox's source. Barring that you need at least two observations of things matching your assumption, before and after population samples showing full fixation rates as high as single-organism mutation rates in order to even begin contesting.

Blogger David F February 19, 2019 1:05 AM  

@112 I am aware of the numbers Vox brought up in Maximal Mutations, yes. I looked at the results of his calculations, thought "that can't possibly be right", and went in search of the original studies. I note that Vox made no effort to link to his source, and I had to dig it up myself.

Vox's numbers are flat-out wrong because they do not account for the differences in the rate of mutation per generation between the bacteria under study and humans.

If you want observations, here:
1) Human mutation rate per birth: approximately 30 (with large error bars), measured by sequencing of a child and both their parents.
2) Human rate of genetic disorders: approximately 2.5% of births (most of these are not related to point mutations, but I'll let that slide to simplify things.)
3) Net result: less than .1% of mutations in humans are substantially deleterious.

Conclusion: most point mutations in humans are neutral, or close enough to neutral as to not create a large deviation from the math.

That brings us right back to:
(u * Ne) * (1 / Ne) = u

Fixation is not only proportional to mutation (sufficient in itself to demolish Vox's math), it proceeds at approximately the same rate.

Blogger wreckage February 19, 2019 1:36 AM  

@113 are you going to link your source, then? Your assumptions on mutation rate are derived from observation, yes?
Are they congruous with any of these models?
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2871823/

Blogger David F February 19, 2019 2:27 AM  

@114 The bulk of my numbers come from an article that jumps off from a study that appears to be Vox's reference on the bacteria numbers:
http://book.bionumbers.org/what-is-the-mutation-rate-during-genome-replication/

Follow the links to see the studies in question.

The defect rate of 2.5% came from a quick hunt via google, and I found several instances with similar numbers. The first hit:
https://www.rightdiagnosis.com/g/genetic/stats.htm

In the previous thread, Crew found a useful article on the differences between the chimp and human genome:
https://sandwalk.blogspot.com/2012/01/whats-difference-between-human-and.html

According to the above, the 30 million mutations Vox cites are the number of "single nucleotide differences between human and chimp genomes", ie, point mutations.

The paper you cite introduces far more complexity than necessary to deal with Vox's calculations. I skimmed it and didn't see anything that suggested the genetic model was in crisis, and in any case it's primarily an overview. I did follow a few of the links, one of the papers did some interesting work on an E. coli strain with damaged splice-repair mechanisms that mutates very readily. Unsurprisingly, fitness falls in those circumstances (especially with repeated restrictions to a single survivor to vastly increase the odds of fixing deleterious mutations). I don't think it's a good model for point mutation fitness calculations, however, as I suspect most of the mutations will be splice errors instead of the single base-pair errors used for the genetic drift clock.


Bonus cite for Azure:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4503671/
Direct observation of a fitness-increasing mutation carrying neutral mutations to fixation.

Blogger wreckage February 19, 2019 6:08 AM  

"I skimmed it and didn't see anything that suggested the genetic model was in crisis"

Sure, that's not the point of the paper. I was trying to get a quick overview of the state of the modelling, so I could get a basic handle on the assumptions in play and try to see how far the walk was between that, and Vox's simplified model. But, my statistics-fu is not strong enough to do that quickly or simply.

I am therefore unable to make a comparison of the models that meets my own standards for armchair punditry.

Blogger Azure Amaranthine February 19, 2019 9:37 AM  

" I looked at the results of his calculations, thought "that can't possibly be right", and went in search of the original studies."

That's where you thought wrong.

"Fixation is not only proportional to mutation"

You have yet to provide any evidence whatsoever for that other than just-so stories.

"Vox's numbers are flat-out wrong because they do not account for the differences in the rate of mutation per generation between the bacteria under study and humans."

*Headdeask*.

Okay, you're an irretrievable retard and I forsake you.

Blogger KPKinSunnyPhiladelphia February 19, 2019 11:56 AM  

Azure Amaranthine wrote:"By those criteria, you would have to shut down every population genetics lab on the planet."

If that's all they're contingent on, that's a feature.

"It's math. Applied math. And it's right."

It is not applied in the slightest.

If it contradicts observed reality it is also wrong.

If it is based on extra-scientific philosophy it is also irrelevant.


You are commiting a classic fallacy here: just because something isn't observed -- or can never be observed because it's part of the irreproducible past -- doesn't mean it's not true.

Sometime in the very very distant future, the expanding universe will have caused all of the distant celestial objects to be SO far away that their light can never reach us. A sentient being then, looking at the sky, will see only local objects. If he concludes, by observation, that that is all there is, he will be incorrect.

Granted, it is true that a contrary hypothesis -- "there are things out there we can't see" -- is not scientific in the Popperian sense that it can't be falsified. But if our sentient being has high level math at his disposal, he can create very plausible inferences.

By the way, such plausible inferences are why we have the modern world today. You would not be able to type at your computer and send what your write around the world without the applied math derived from quantum mechanics.

Blogger Azure Amaranthine February 19, 2019 1:07 PM  

"You are commiting a classic fallacy here: just because something isn't observed -- or can never be observed because it's part of the irreproducible past -- doesn't mean it's not true."


Pfffthahaha. Dude, do you realize what you just said that as subtext of? You're also trying to strawman what I actually said.

Blogger Azure Amaranthine February 19, 2019 1:25 PM  

The irony is that that exact argument is used by Darwinians against any form of Design. It can only even be made once the philosophical claims of material naturalism have been accepted dogmatically.

The strawman is that I didn't say that just because something isn't observed it isn't true. I said that when something is inferred rather than observed and contradicts something that is observed, there is obviously something wrong with the inference.

Blogger KPKinSunnyPhiladelphia February 19, 2019 3:45 PM  

Azure Amaranthine wrote:"You are commiting a classic fallacy here: just because something isn't observed -- or can never be observed because it's part of the irreproducible past -- doesn't mean it's not true."

Pfffthahaha. Dude, do you realize what you just said that as subtext of? You're also trying to strawman what I actually said.


You DID write "if it contradicts observed reality, it is also wrong."

I read those words literally. If you expected me to infer another message -- and I have a suspicion about what you did mean, given your response -- you need to write more clearly.

Yes, an only locally observerd universe DOES NOT invalidate the prospect of portions of the universe that are "unobservable," but the argument for that is purely theoretical, because it can only be understood mathematically. And it will very likely be unfalsifiable.

VD's contention that the arithmetic of gene fixation that makes TENS suspect depends on a key assumption: that speciation and species development is a stochastic process. If it is, he probably wins the argument. If it isn't, then we still have a lot to learn.

And in genetics, we still have a WHOLE lot ot learn -- assuming we can.

Blogger Azure Amaranthine February 19, 2019 6:54 PM  

"You DID write "if it contradicts observed reality, it is also wrong."

I read those words literally."


How the hell do you get off parsing that as "if I don't see it it doesn't exist"?

You're being dishonest. Stop it. No one is fooled.

This is the difference between saying:

A: "I see a sphere and you're calling it a cube therefore you are lying."

And,

B: "I can't see any cube from the other side of this wall between me and you, therefore you're lying."

"And in genetics, we still have a WHOLE lot ot learn -- assuming we can."

Agreed.

That being said, Vox cited his evidence. You need to either falsify it, or find/cite observations to the contrary.

Simulations do not disprove reality, regardless how attractive the glamor.

Blogger David F February 19, 2019 10:11 PM  

@117 Azure Amaranthine wrote:You have yet to provide any evidence whatsoever for that other than just-so stories.
The math I have provided is much more than a just-so story. So far you've done nothing but complain about it without substance. Show me where it is wrong.

And we're back to ad hominem, with no math to be seen from you. Vox's math is as wrong as is his obsession with series versus parallel fixation.

An observation, if you care to look: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4503671/
Multiple lines of bacteria, sequenced at various stages, showing the progress to fixation of various mutations. In parallel, with graphs to show it.

Blogger David F February 19, 2019 10:22 PM  

@116 wreckage wrote:I was trying to get a quick overview of the state of the modelling, so I could get a basic handle on the assumptions in play and try to see how far the walk was between that, and Vox's simplified model. But, my statistics-fu is not strong enough to do that quickly or simply.

Mutation is a huge and complex subject. Vox took a single ten year old study on bacteria and tried to generalize it to human fixation rates. Without considering differences between bacteria and human mutation rates.

Simplifying the problem, Vox's 30 million appears to be the number of point mutations between chimps and humans when comparing genomes (see https://sandwalk.blogspot.com/2012/01/whats-difference-between-human-and.html).

Vox's calculation assumes the fixation rate per generation in bacteria is the same as in humans. The fact that humans produce mutations at 100,000 times the rate of the bacteria in question needs to be accounted for. See wikipedia's page on fixation (population genetics) for the equation, but the result is simple: fixation rate is equal to the mutation rate.

So far, nobody on Vox's side of this argument has produced any reason to believe the fixation rate math is incorrect. They've complained about it a bunch, and made vague suggestions about thresholds, but no mathematical counter-argument has been attempted.

Anonymous Anonymous February 19, 2019 11:29 PM  

David Fenger wrote:Vox's calculation assumes the fixation rate per generation in bacteria is the same as in humans. The fact that humans produce mutations at 100,000 times the rate of the bacteria in question needs to be accounted for. See wikipedia's page on fixation (population genetics) for the equation, but the result is simple: fixation rate is equal to the mutation rate.

You didn't read. Vox accounted for that. In fact he went so far as to create a model which created an artificial impossible maximum of mutations per generation in mammals, based on a series of minimum viable populations. And the numbers still didn't fit evolutionary timelines.

Azhure is right - you don't have sufficient reading comprehension even if it is apparent you can do a bit of math.

Blogger Azure Amaranthine February 19, 2019 11:32 PM  

"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4503671/"

Let's keep it simple. Just read the author summary where they specifically state that this is not genetic drift.

No need to get more complex than that to point out that once again you present irrelevancies. This is an experiment on molecular clock theory in adaptive evolution.

Thus proving once again your illiteracy.

Blogger David F February 19, 2019 11:33 PM  

@125 There's no need for minimum viable populations. The rate of drift via the standard model is sufficient to account for the mutations. Vox just got the math wrong. By five orders of magnitude.

Blogger SirHamster February 20, 2019 1:46 AM  

David Fenger wrote:So far, nobody on Vox's side of this argument has produced any reason to believe the fixation rate math is incorrect.

The Gamma liar creates a false frame and declares victory.

YclepedBobAli wrote:Azhure is right - you don't have sufficient reading comprehension even if it is apparent you can do a bit of math.

Torturing numbers is not doing math.

Blogger David F February 20, 2019 2:20 AM  

@128 Show me the lie. The standard model explanation laid out simply once more:

1) The rate of fixation for a mutation not subject to selection is simply the rate of introduction of such mutations.
(https://en.wikipedia.org/wiki/Fixation_(population_genetics)
2) Mutation rate for humans is roughly the same per base pair per replication as the bacteria Vox uses.
(http://book.bionumbers.org/what-is-the-mutation-rate-during-genome-replication/)
3) The human genome is 1000x as large as the bacteria's.
4) Human zygote-to-zygote generation requires on average 100 replications.
5) Thus, the human mutation rate is 100,000 times higher than the bacteria in question.
6) by (1), that gives us a fixation rate 100,000 times higher than the bacteria.

That gets us from Vox's 125 mutations in 450,000 generations to 12.5 Million.

No torture required, just basic math.

I'll grant the fixation rate = mutation rate thing feels counterintuitive, and takes some basic probability theory to grasp. That's why I wrote the sim, to confirm to myself that the fixation rate equation held at various scales.

Blogger David F February 20, 2019 2:33 AM  

@126 The conclusion of the article (last paragraph of Discussion):

"We experimentally demonstrated that hitchhiking ensured that the molecular clock for neutral mutations in fitness-increasing evolution occurred at the same rate as expected for genetic drift in neutral or fitness-steady evolution. The extension of the molecular clock, which has been verified for neutral evolution, to adaptive evolutions can provide insights into the past environment. Genetic drift, which requires the suppression of adaptive mutations over a long generation time, has led us to suppose that the past environment was sufficiently steady that the fitness contributions of fixed mutations could quickly change from positive to neutral by diminishing returns, leading to fitness-steady or neutral evolution. However, if the hitchhike-driven molecular clock runs for neutral mutations, adaptive mutations may occur frequently. Thus, it is reasonable to propose that the past environment was not always so steady but underwent dynamic changes that allowed organisms to adaptively evolve according to the hitchhike-driven molecular clock."

None of that supports your interpretation. This work shows that in an environment where the organism is experiencing fitness-increasing evolution, the drive to fixation of the fitness-increasing mutations (which fix much more quickly than neutral mutations) can carry hitchhiker neutrals to fixation as well. This *increases* the rate over that suggested by genetic drift alone.

It also graphically shows fixation happening in parallel.

Blogger Azure Amaranthine February 20, 2019 12:07 PM  

Still not genetic drift, Fenger. Even if I allowed you that the entire observation were not irrelevant to your point, you still either can't or did not read, as is shown by your failure to grasp what they actually experimented on and their outcome.

Do you know what Molecular Clock means? Do you understand its limitations? Heck, just bring up the wiki article, scroll down to the non-constant rate section.

Now look at their actual recorded rate of mutation fixation via synonymous hitchhiking in a selective environment, and note that it's less than a tenth of rate of accumulation of mutations. The non-synonymous fixation rate that makes up the rest of the neutral mutations is six orders of magnitude lower than even that.

Now look a bit lower than that, just two paragraphs above the Discussion section, and note that they did not actually report the rate of neutral fixation. They assumed it to be similar to the theoretical spontaneous mutation rate.

Reading on into the Discussion you're attempting to cherry pick from,

"As neutral mutations accumulate on all genomes in a population spontaneously with equal probability, regardless of which genome gains an adaptive mutation to propagate or when, the fixation rate of the neutral mutations should coincide with the spontaneous mutation accumulation rate, suggesting that hitchhiking..."

"To understand how the three categories of mutations participate in the dynamics of the molecular clock, we firstly assumed that every genome spontaneously accumulated the neutral mutations at the following rate:"


They assumed in all cases within the paper that the fixation rate due to GD is the same a the spontaneous mutation rate in a single organism, despite reporting rates less than 8% of that. Via hitchhiking with adaptive mutations (read: selection pressures and population size manipulation).

To carry the obvious objections to your assumed math from the former thread:

#1: You must assume that the entire genome is room for neutral mutations. In reality at least twenty percent, but more likely sixty to eighty percent is not.

#2: You must assume that none of the spontaneous mutations whatsoever affect already mutated or fixed sites.

#3: No adaptive advantages can be either acquired or accumulated by neutral mutation, which rules out most if not all phenotypic expressions.

#4: 12.5m is still millions away from 15m, even after assuming that there are no deleterious/repetitive/phenotyping mutations whatsoever. This is a literally impossible gap to bridge for your model, considering the math involved.

And here's a new one:

#5: The actual number needed is closer to 19.5m according to newer studies which put the gap at 39m.


Finally, I'm done with you Fenger. I will not respond to you any more. All you do is lie and report irrelevancies.

Blogger SirHamster February 20, 2019 6:29 PM  

David Fenger wrote:Show me the lie.

SirHamster wrote:David Fenger wrote:So far, nobody on Vox's side of this argument has produced any reason to believe the fixation rate math is incorrect.

You said nobody has produced any reason to disbelieve your math. That is a lie. Multiple people have objected to the math. Notably, Vox responded directly to you.

VD wrote:This is the part that is completely wrong: 30 mutations per offspring = 30 fixations per generation..

Pointing out that 1 + 1 = 3 is wrong is a reason to believe that the math is incorrect.

That you make a blatantly false statement about the state of the discussion demonstrates that you are a rhetoric speaker and not very smart.

Blogger David F February 21, 2019 12:27 AM  

@132 Vox's response offered no explanation whatsoever. It's simply a bald claim with nothing whatsoever to back it up.

That neutral mutations fix at a rate equal to their introduction is the standard explanation offered by genetics. That one statement puts lie to Vox's claim that the genetic model cannot explain the number of mutations between chimps and humans. It can, it does, and (u*Ne)*(1/Ne) = u is exactly how it does so.

Yet again:
1) Bacteria: 25 fixations per 40,000 generations (Vox's starting point, "Nature 2009")
2) Vox projects this to 450,000 generations since the chimp-human last ancestor, somehow getting 125 as the 'maximum mutations'. (9e6 / (1600*20) = 281, so I don't know where 125 came from. Presumably an earlier draft where he'd used the lower 4 million year estimate for CHLA.)
3) Humans have roughly the same mutation rate *per base pair per replication* as those bacteria, but about 1000x as many base pairs, and around 100 replications per generation.
4) The standard model for the mapping between neutral mutation rates and neutral fixation rates gives a linear relationship between the two.
5) Multiply 281 by 100,000, you get about 28 million mutations expected.

More than enough, since the chimp line gets to contribute too.

You may not like the math for the fixation of neutral mutations, but that does not change that it is a standard part of the model for those 30 million mutations. (cf Wikipedia, Fixation (population genetics)) If you wish to challenge it, do so directly, and show your math.


Blogger David F February 21, 2019 12:58 AM  

@131 Your first quote is part of a larger statement, and taken badly out of context. It is stating the expected rate of neutral mutation, and goes on to say: "This is the first experimental demonstration of the molecular clock with the same rate as the spontaneous mutation accumulation rate."

They *measured* the rate of mutation and the rate of fixation, and found that the rate of fixation under positive selection was the same as that expected for the molecular clock. The point of their study is that the molecular clock runs at the same rate under selective pressure as during times of relative stasis.

Your second quote is an assumption that informs their model of mutation: R_Neutral_Genome = u*L*(1-alpha-beta)

They go on to determine the values in that relationship experimentally. Hunting through the text for 'assume' and 'should' doesn't invalidate the work.

#1 I (and the paper above) do not assume the entire genome is neutral. They explicitly have a term for the negative mutation rate, and compute it from their results. After a little digging I found thier beta: 0.42. 42% of mutations were negative, and the math still worked. (They note that this is a higher than normal rate, as they'd placed the bacteria under severe environmental pressure.)

#2 There is no assumption that mutations don't overlap. Multiple instances of the same mutation at the same site add to the population of that mutation, increasing the odds of fixation, and the math comes out the same. As to fixed sites, only 2% of the genome differs between chimps and humans, so hits on those reduce the total by at most 2%.

#3 That's kind of the point of neutral mutation. I am making no effort to explain the phenotypic differences between humans and chimps, just the number of accumulated mutations.

#4 Vox bungled his math on the 125: 9,000,000 divided by 32,000 is 281.25, not 125. So my back of the envelope, rough calculation with error bars big enough to drive a truck through, gets 28 million mutations on the human side of the CHLA, substantially more than measured. So sure, knock 42% off for negative mutations, and another 2% for already-fixed sites. 56% of 28 million is 15 million.

#5 See above. 42% is a bit on the high side according to the paper, so let's drop that to 30% losses to negative mutations and remutation of fixations. 70% of 28 million is 19.6 million.



Blogger SirHamster February 21, 2019 1:39 AM  

David Fenger wrote:@132 Vox's response offered no explanation whatsoever. It's simply a bald claim with nothing whatsoever to back it up.

You're dumb. I pre-empted this line of evasion.

SirHamster wrote:Pointing out that 1 + 1 = 3 is wrong is a reason to believe that the math is incorrect.

Vox doesn't owe you an explanation. "I don't understand that reason" doesn't make a reason stop being a reason.

Blogger Azure Amaranthine February 21, 2019 3:44 AM  

Literally unable to read the numbers because he wants to believe the assumptions that they don't support. Still outright lying -- or incredibly stupid.

Blogger David F February 21, 2019 11:30 AM  

@135 The mathematics of neutral drift state exactly what I said. In the long term, if there are 30 mutations per birth, there will be 30 fixations per generation.

Saying "that's wrong" doesn't change that that's exactly what the equation says. Trying to argue that "science can't explain X" when I've presented exactly how the modern synthesis *does* explain X is even worse.

(u*Ne)*(1/Ne) = u.

u = 30 for humans.
Ne = well, it doesn't much matter, really. Call it a million for most of those 9 million years, that's more than chimps have now.
30*1000000 = 30 million new mutations every generation.
1/100000 = 1 in 1 million chance that a new neutral mutation will eventually fix.
Result: 30 fixations per generation, on average.

One does need to account for losses to deleterious mutations, but as I note above, there's a fair bit of room for that while still hitting 15 million.

Show your work. Just saying "wrong" isn't helpful.

Blogger SirHamster February 21, 2019 2:25 PM  

David Fenger wrote:Show your work. Just saying "wrong" isn't helpful.

You are dishonest and stupid. Saying "wrong" is helpful.

Your demand for work is dishonest as you dismiss all responses. You then repeat yourself and act like no one responded.

Tedious atheist/evolutionist NPC.

Blogger David F February 21, 2019 6:17 PM  

@138 Nobody has tried to actually argue with the math, just dismiss it out of hand.

Blogger SirHamster February 21, 2019 6:41 PM  

David Fenger wrote:@138 Nobody has tried to actually argue with the math, just dismiss it out of hand.

Gamma won't stop lying. Multiple people have questioned the assumptions your math is built on.

You are a dishonest and stupid person whose only tactic is to pretend rationality while lying repeatedly.

Arguing with you is a waste of time.

Blogger David F February 22, 2019 12:29 AM  

@140 There've been some vague objections from Azure about the rate of neutral mutations. Nothing else even remotely substantive.

Vox's calculation does not account for the difference in mutation rates. The standard genetic model says fixation rate is proportional to mutation rate.

Which of those statements is a lie?

Blogger Azure Amaranthine February 22, 2019 2:08 AM  

Lying it is.

Blogger damaris.tighe February 22, 2019 3:14 AM  

Passing this on:

In a world where we have perfect information available, it's an idea that can be investigated. But it's a methodological approach that is completely redundant.

What we do have presently is comparative sequencing between living individuals in a genetic line. Child -> Parent -> Grandparent -> Great-Grandparent.
Independent tests show that the error rate in replicating DNA is about 70 base pairs per generation in humans, on average. This isn't to do with gene mixing between the parents, this is about errors in the sequence replication caused by deletion, insertion, or switching of (usually) single nucleotides within the sequence. Think of it like the photocopy effect - noise introduced in the replication process.

This means that a child has on average 70bp of DNA that is different from their parents due to errors in DNA replication, 140bp of variation from their grandparents, and 210bp of variation from their great-grandparents etc..It takes 7 generational leaps to reach an error accumulation level of 490 base pairs, which is comparable to the challenger's expectation of change to be demonstrated on a species wide level. I don't know that there are any families that have that many living generations, but the trend is verifiable and there's no reason to think the data can't be extrapolated upon. Also, study of this principle doesn't need to be restricted to humans to demonstrate the mechanism.

There are similar replication errors in other organisms with much quicker generational cycles that demonstrate this principle on a longer generational scale.
https://en.wikipedia.org/wiki/Mutation_rate
This is what evolution is. Random mutation that is accumulated among individuals generationally, and the mutations that produce an expressed difference in the individual can be acted upon by natural selection which will then select for those changes either positively or negatively (meaning they will either propagate throughout the species' gene-pool down the generations, or they will not).

Back to the human example.
Let's just take a couple of straightforward bits of genetic data and make a slapdash "back of the envelope" prediction.
Take the error rate in genetic replication of 70 base-pairs per generation.
Let's assume generations are 20 years apart to keep the math simple. Seems overly conservative given most of human history, but it'll do.
Sequencing data shows that the human genome differs from the chimpanzee genome by 35 million base pairs in the parts of the genome that is present in both species.
So how many generations (and therefore years) does it take for replication errors to accumulate to 35 million bp of variation?

35,000,000 bp divided by 70 bp = 500,000 cycles (generations)
If 1 cycle/generation = 20 years,
then 500,000 generations = 10,000,000 years.
So, you can predict just from the observations of the error rate in DNA replication over generations, and the variation between the shared human and chimpanzee genome, that it would take 10 million years for our species to vary from chimpanzees by 35 million base pairs. So we should expect our common ancestor to have lived about 10 million years ago.

That's just one conclusion using one method. We need independent evidence that converges on a similar figure to increase our confidence in that conclusion.
https://en.wikipedia.org/wiki/List_of_human_evolution_fossils
It's helpful that fossil evidence comes up with a comparable figure.
This prediction was using a very crude methodology that no scientist would publish because of the lack of care and rigour it was done with. But even using this crude method you can get a picture of how the mechanism functions over the long term, and how it works to support a conclusion about human-chimp evolution that other independent studies and methodologies have found.

Blogger Azure Amaranthine February 22, 2019 7:42 AM  

This is already more specific than that, Damaris.

Blogger Azure Amaranthine February 22, 2019 7:46 AM  

"Seems overly conservative given most of human history, but it'll do."

It's not just about the birth of the first child. It's about the time to the average birth of all of the children, in which case I can't speak for chimps, but 20 years is almost certainly too fast for humans, even in conditions where the average lifespan was something less than fifty years.

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