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Author Topic:   Micro v. Macro Creationist Challenge
caffeine
Member (Idle past 1024 days)
Posts: 1800
From: Prague, Czech Republic
Joined: 10-22-2008


(2)
Message 31 of 252 (813149)
06-23-2017 4:35 PM
Reply to: Message 12 by aristotle
06-16-2017 4:19 AM


I don't normally like to jump on when there's already a pile of other posters, but in this case I think everyone else has overlooked a fundamental misunderstanding:
That asked, the chances of the mutations required between human and primate, occurring in the right gene and often enough in the population to change the genome of the entire species, are next to naught.
A specific mutation doesn't need to happen often to become characteristic of a species. It only needs to happen once. It can then spread throughout the population by inheritance.
If it's an advantageous mutation, then it's likely to spread much more quickly than if not. When we talk about an advantageous mutation, all we really mean is one whose possessors are liable to leave more children in the next generation than those without. So each successive generation a higher proportion of the population will possess this mutated form of the gene; even though the mutation only happened once.
That's what natural selection is.
Edited by caffeine, : No reason given.

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CRR
Member (Idle past 2242 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 32 of 252 (813305)
06-26-2017 12:23 AM
Reply to: Message 31 by caffeine
06-23-2017 4:35 PM


advantageous mutations
If it's an advantageous mutation, then it's likely to spread much more quickly than if not
Advantageous mutations are subject to the cost of selection (Haldane's Dilemma) which limits how many advantageous mutations can be fixed in the time available. Since the publication of ReMine’s book in 1993, there has been no serious dispute that Haldane’s analysis (if correct) places a 1,667 limit, a severe limit, on human evolution, assuming 10 million years since the last common ancestor.
Ian Musgrave in Haldane's non-dilemma does not dispute this limit but argues that humans are ~240 genes away from the last common ancestor and ~594 genes away from the chimp. However this ignores beneficial changes in the regulatory DNA which could well have been an order of magnitude, or more, higher.
This limit has led to neutral theory which allows a much larger number of neutral mutations to be fixed in the same time. However most neutral mutations have no affect on the phenotype (that's why they're neutral) so we are really stuck with the 1,667 limit for humans, and perhaps 2,500 for chimps, explaining differences between the two species. These numbers reduce if the time to the last common ancestor is less than 10 million years.
A specific mutation doesn't need to happen often to become characteristic of a species. It only needs to happen once.
Even advantageous mutations are unlikely to be fixed unless the selection coefficient is fairly high. In most cases the selection coefficient is small and hence most advantageous mutations are likely to be lost. But you're right, it only needs to happen once; then be very lucky. In many cases drift will swamp selection.

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Coyote
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(1)
Message 33 of 252 (813324)
06-26-2017 9:39 AM
Reply to: Message 32 by CRR
06-26-2017 12:23 AM


Re: advantageous mutations
From TalkOrigins:
Claim CB121:
J. B. S. Haldane calculated that new genes become fixed only after 300 generations due to the cost of natural selection (Haldane 1957). Since humans and apes differ in 4.8 107 genes, there has not been enough time for difference to accumulate. Only 1,667 nucleotide substitutions in genes could have occurred if their divergence was ten million years ago.
Source:
ReMine, Walter J., 1993. The Biotic Message, St. Paul Science, Inc.
Response:
Haldane's "cost of natural selection" stemmed from an invalid simplifying assumption in his calculations. He divided by a fitness constant in a way that invalidated his assumption of constant population size, and his cost of selection is an artifact of the changed population size. He also assumed that two mutations would take twice as long to reach fixation as one, but because of sexual recombination, the two can be selected simultaneously and both reach fixation sooner. With corrected calculations, the cost disappears (Wallace 1991; Williams n.d.).
Haldane's paper was published in 1957, and Haldane himself said, "I am quite aware that my conclusions will probably need drastic revision" (Haldane 1957, 523). It is irresponsible not to consider the revision that has occurred in the forty years since his paper was published.
ReMine (1993), who promotes the claim, makes several invalid assumptions. His model is contradicted by the following:
--The vast majority of differences would probably be due to genetic drift, not selection.
--Many genes would have been linked with genes that are selected and thus would have hitchhiked with them to fixation.
--Many mutations, such as those due to unequal crossing over, affect more than one codon.
--Human and ape genes both would be diverging from the common ancestor, doubling the difference.
--ReMine's computer simulation supposedly showing the negative influence of Haldane's dilemma assumed a population size of only six (Musgrave 1999).
CB121: Haldane's Dilemma

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Tangle
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Posts: 9489
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Member Rating: 4.9


(1)
Message 34 of 252 (813325)
06-26-2017 10:04 AM
Reply to: Message 32 by CRR
06-26-2017 12:23 AM


Re: advantageous mutations
CRR writes:
Ian Musgrave in Haldane's non-dilemma does not dispute this limit but argues that humans are ~240 genes away from the last common ancestor and ~594 genes away from the chimp. However this ignores beneficial changes in the regulatory DNA which could well have been an order of magnitude, or more, higher.
This limit has led to neutral theory which allows a much larger number of neutral mutations to be fixed in the same time. However most neutral mutations have no affect on the phenotype (that's why they're neutral) so we are really stuck with the 1,667 limit for humans, and perhaps 2,500 for chimps, explaining differences between the two species. These numbers reduce if the time to the last common ancestor is less than 10 million years.
What is it about you creationist that make you have to distort what scientists say? Do you think we won't check? Musgrave actually says:
quote:
The above study only covered protein coding genes, not regulatory sequences, and most biologists expect that changes in regulatory sequences played an important role in evolution. Getting at the number of beneficial mutations in regulatory genes that have been fixed by natural selection is a lot harder, but it seems like around 100 regulatory genes may have been selected (Donaldson & Gottgens 2006, Kehrer-Sawatzki & Cooper 2007). Again, even if we set the number of regulatory genes that have been selected as the same number as the most wildly optimistic estimate of protein coding genes fixed by natural selection, then we end up with 960 fixed beneficial mutations, below ReMine’s calculation of Haldane’s limit [5]. This means Haldane’s dilemma is irrelevant to human evolution.
Conclusion: Haldane’s dilemma has never been a problem for evolution, but the technical nature of the arguments involved made it difficult to clearly demonstrate anti-evolutionists misuse of the dilemma. Also, the difficulty in getting the original papers meant that the distortion of Haldane’s work by anti-evolutionists was not obvious.
Now Walter ReMine’s claim that 1667 beneficial mutations is too few to generate a philosopher poet from the common ancestor of chimps and humans is shown to be trivially false from comparison of the human and chimp gemone. As this claim was the keystone of ReMine’s argument, Haldane’s dilemma should disappear as an anti-evolutionist claim.

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Faith is the denial of observation so that Belief can be preserved."
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CRR
Member (Idle past 2242 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 35 of 252 (813345)
06-26-2017 7:17 PM
Reply to: Message 33 by Coyote
06-26-2017 9:39 AM


Re: advantageous mutations
Ah, the ever "reliable" Talk Origins.
Since humans and apes differ in 4.8 10^7 genes ...
There aren't that many genes in humans and apes combined! I assume they meant 4.8 10^7 differences including point substitutions.
Only 1,667 nucleotide substitutions in genes could have occurred if their divergence was ten million years ago.
ReMine specifies beneficial, i.e. subject to natural selection, mutations, which can include point substitutions.
ReMine (1993), who promotes the claim, makes several invalid assumptions. His model is contradicted by the following:
--The vast majority of differences would probably be due to genetic drift, not selection.
--Many genes would have been linked with genes that are selected and thus would have hitchhiked with them to fixation.
--Many mutations, such as those due to unequal crossing over, affect more than one codon.
--Human and ape genes both would be diverging from the common ancestor, doubling the difference.
--ReMine's computer simulation supposedly showing the negative influence of Haldane's dilemma assumed a population size of only six (Musgrave 1999).
--The vast majority of differences would probably be due to genetic drift, not selection.
Which is as I said. However genetic drift applies to neutral mutations which by definition don’t affect the phenotype, hence they are not significant for explaining differences between humans and chimps.
--Many genes would have been linked with genes that are selected and thus would have hitchhiked with them to fixation.
That would actually tend to limit genetic drift to that of actively selected genes. Since ReMine is talking about 1670 beneficial mutations with a much smaller number being in progress at any time this is not going to be significant.
--Many mutations, such as those due to unequal crossing over, affect more than one codon.
Actually I’m not clear what he’s getting at here. Crossing over is a mechanism to partially randomise the distribution of existing genes within the gametes.
--Human and ape genes both would be diverging from the common ancestor, doubling the difference.
Yes. That’s not disputed. It could even be a little higher.
--ReMine's computer simulation supposedly showing the negative influence of Haldane's dilemma assumed a population size of only six (Musgrave 1999)
Actually that is a criticism of ReMine’s use of David Wise's (dwise1?) program MONKEY and is irrelevant to ReMine’s calculations. Musgrave admitted it took him a couple of hours to identify what the error was. However it does also illustrate a flaw in these programs in that they allow the entire population to be replaced with the most successful variant in a single generation. Such programs therefore don’t simulate realistic biological populations.
(Please note I have never used MONKEY myself and I'm going on what is in the TO site)

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CRR
Member (Idle past 2242 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 36 of 252 (813346)
06-26-2017 7:37 PM
Reply to: Message 34 by Tangle
06-26-2017 10:04 AM


Re: advantageous mutations
Getting at the number of beneficial mutations in regulatory genes that have been fixed by natural selection is a lot harder, but it seems like around 100 regulatory genes may have been selected (Donaldson & Gottgens 2006, Kehrer-Sawatzki & Cooper 2007).
The conclusions from the ENCODE pilot project were published in June 2007 and a lot has changed since then.
In note [3] Musgrave says "Current evidence is that around 1.2% of the genome codes for protein, about the same amount for structural RNA and another 5% for regulatory sequences." So even in 2007 we could expect for each new gene 4 times as much change in the regulatory DNA. It's likely the real number is much higher than the 100 identified in 2007.
And as I pointed out each new gene probably resulted from a number beneficial mutations.
Actually, are evolutionary mechanisms even sufficient to produce over 100 new genes in the time available?

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Tanypteryx
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Posts: 4344
From: Oregon, USA
Joined: 08-27-2006
Member Rating: 5.9


Message 37 of 252 (813347)
06-26-2017 8:13 PM
Reply to: Message 35 by CRR
06-26-2017 7:17 PM


Re: advantageous mutations
--The vast majority of differences would probably be due to genetic drift, not selection.
Which is as I said. However genetic drift applies to neutral mutations which by definition don’t affect the phenotype, hence they are not significant for explaining differences between humans and chimps.
I have seen you make this statement several times about neutral mutations. This is incorrect.
Neutral mutations are neutral with respect to fitness, they are not selected out of the population.
They may indeed affect the phenotype without being selected for or against. At some future time the changes to the phenotype may be affected by natural selection.

What if Eleanor Roosevelt had wings? -- Monty Python
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dwise1
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Posts: 5930
Joined: 05-02-2006
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Message 38 of 252 (813348)
06-26-2017 9:32 PM
Reply to: Message 35 by CRR
06-26-2017 7:17 PM


Re: Everybody's got something to hide, except for me and my MONKEY
My page about MONKEY is at cre-ev.dwise1.net/monkey.html. I have also written about it in this forum, so you could do a search.
Such programs therefore don’t simulate realistic biological populations.
Neither WEASEL nor MONKEY were ever intended to. I highly recommend that you read my MONKEY page before you make more false assumptions.
When Dawkins described WEASEL, I couldn't believe it, so I had to test it. Since Dawkins didn't provide any source code (I think it was a form of BASIC running on a MacIntosh), the only way I could test it was to write my own. In order for it to run as exactly like his as possible, I used his description of the program to come up with a specification for mine. I wrote it in Turbo Pascal, since that was what I was working in at the time (1990). It took Dawkins' program the lunch hour to run, but I think that was because he used an interpreted language. Mine succeeded in less than a minute. I ran it repeatedly and it succeeded repeatedly, every time without fail. I still couldn't believe it, so I calculated the probabilities involved. As improbable as each individual step is, the probability that every single step would fail becomes smaller and smaller until it is virtually impossible for it to fail. I wrote those calculations up in a text file, MPROBS.DOC, which I included in a PKARC package and uploaded it to CompuServe. The rest is history, including the part where I ported it over to C.
Again, it is not a simulation of evolution! Rather, it is a comparison of two different selection methods. Re-read the first half of Chapter 3, "Accumulating Small Changes", from Dawkins' book, The Blind Watchmaker, where he describes two different kinds of selection to use to get a desired string:
  1. Single-step selection in which the entire final product is generated at one time and must match the target in order to succeed. If it fails, then the next trial must start all over again from scratch.
    This is the kind of selection that creationists think that evolution uses and they base all their probability arguments on it. They are completely wrong and hence their probability arguments are rubbish.
  2. Cumulative selection which is an iterative method. You start with a randomly generated attempt, but when that fails instead of throwing it away you make multiple copies of it with slight random changes ("mutations"), so that those copies are very similar to, yet slightly different from, the original, analogous to what happens in nature. Then you select the copy that comes closest to the target and use it to generate the next "generation" of copies. And so on.
    This comes much closer to describing selection as used by evolution (of course, since it was modeled after actual evolutionary selection).
So what WEASEL and MONKEY do is to compare how well those two selection methods work by giving them both the same problem to solve. Everything is kept the same except for the selection method. Single-step selection fails abysmally while it is virtually impossible for cumulative selection to fail. And the probability calculations in MPROBS explain why.
I recently added to the end of the page a brief discussion of programs which do try to model evolution. I also found that some creationists misrepresent how WEASEL works; I discuss that too. If you want to claim that Royal Truman is correct, then I invite you to show me in my source code and in my probability calculations where I am supposed to have done what he claims we do. Like I say, "Everybody's got something to hide, except for me and my monkey!"
Keep in mind that when I wrote MONKEY, we were still using XT clones. Most PCs now are at least hundreds of times faster, if not thousands of times. So when you run MONKEY, it will appear to succeed instantaneously. In order to observe the progressing towards and regressing away from the goal, pick a smaller number of offspring generated per iteration.
Here is Ian Musgrave's email to me about it back when all this was going down. As you can see, that was nearly 20 years ago. I remember having received a xerox copy of what Remine wrote about me and my MONKEY and I remember being amazed at how much he had misunderstood it.
BTW, I had written MONKEY about a decade before this and posted it in a library on CompuServe where it was constantly downloaded at least once a month for years thereafter. I explicitly asked for feedback and got none except that my numbering of the Markovian chain steps in MPROBS was off by one, and spurious complaints about teleological assumptions in my fitness test which both I and even Dawkins in his original presentation discussed and showed to be irrelevant -- ie, since the single-step selection model made the exact same fitness test, when why was it such an abysmal failure when cumulative selection was such a resounding success?
quote:
Subj: Re: MONKEY
Date: 15-Sep-99 22:01:35 Pacific Daylight Time
From: ********@******.****.***.** (Ian Musgrave & Peta O'Donohue)
To: **********.***
G'DAy David
At 21:31 13/09/99 EDT, you wrote:
>>> have come across your pascal program and was most impressed. May I have
>permission to link to your web page on this subject, and to make available
>the executable and source code to your program?<<
>
>Yes, certainly you may. Out of curiosity, may I ask how you had acquired
it?
> I think that I had uploaded onto two CompuServe forums almost ten years
ago.
> Your email and one I received last year are about the only feedback I have
>gotten about it.
I got it from Robert Williams <****@****.***>, to whom you passed it on
after you answered his query to the NSCE.
You may or may not know that Walter ReMine, in various internet forums (eg
talk.origins and sci.bio.evolution) and in his self published book "The
Biotic Message", claims that your simulation provides a clear example of
Haldanes dilemma. As Haldanes dilemma relates to the rate of fixation of
benefical gene substitutions in a population with a large genome ( > 50,000
or so genes, see http://www.gate.net/~rwms/haldane1.html for some details),
most people were fairly certain that this was not the case. However, Mr.
ReMine would never give details in the internet fora, and only say that the
program and output were detailed in the book. As this is a self published
book, it is actually quite hard to get a hold of. Fortunately, some-one did
get a hold of it, and the program he referenced was yours.
Quote:
" On p 235, n 52, ReMine states "David Wise's simulation, for the IBM
compatible PC under DOS, is circulated by the National Center for Science
Education - a major anti-creation organization." ... ReMine never names the
Wise program, though he does give a reference to the program's
documentation "(Wise, D., 1989)". There is no such listing in ReMine's
References section, but that's the sort of thing that happens to us
all."
Well, I ran your program, and as I expected, it doesn't demonstrate
Haldanes dilema. (It is a lovely version of the program, and super fast,
and I will be honoured to place it on my web site.)
As to the resolution of Mr. ReMine claim. Well, it turns out to be blinding
simple. Here is a quote from the relevant section of ReMines book.
p 235
"That method of mutation is not true to nature [used by Dawkins]. In nature
nothing counts mutations and assures exactly one in each progeny. A more
realistic type of mutation should be used in the simulation so that each
letter has a _probability_ of mutation. Suppose we use this correct method
of mutation while leaving the "average" rate unchanged (at 1 chance in 28).
This subtle correction to the simulation nearly doubles the time needed to
evolve the target phrase: to 86 generations."
p 236
"Then we reduce the reproduction rate to that of the higher vertebrates, say
to n=6. In a sexual species this would require the females to produce 12
offspring each. This is overly optimistic for many species. The simulation
then goes into error catastrophe and does not reach the target phrase. We
can eliminate the error catastrophe by lowering the mutation rate.
"Then by exploration we can find the mutation rate that produces the fastest
evolution. [footnote: in this case the optimum mutation rate is one in 56.]
With this optimal mutation rate, on average, the target phrase is reached in
1663 generations - that is 62 generations per substitution.
"Thus the simulation - with its numerous unrealistic assumptions that favor
evolution - is less than five times faster than haldane's estimate of 300
generations per substitution. Ironically, this suggests that Haldane was
too optimistic about the speed of evolution."
Can you see where ReMine has made his error? I actually wasted a couple of
hours comparing the effects of mutation rates on different programs before
I realized it, but it should have been blindingly obvious.
Here's the key line:
"Then we reduce the reproduction rate to that of the higher vertebrates,
say to n=6"
Well knock me down with a stick of mortadella and call me Jake. ReMine
doesn't know how these programs work. In your program, Dawkins original,
Wesley Elseberry's weasle.pl and my WEASLE4.BAS the "reproduction rate", ie
number of offspring, IS ALSO THE POPULATION SIZE!!!! Of course you will see
only slow substitution in any of these programs when you only have 5
offspring, as there is only a TOTAL POPULATION of 5 strings at any one time.
ReMines argument totally collapses, without even having to point out the
other, obvious problems.
>I had also written an analysis of the mathematics involved. I think I
called
>the text file MPROBS.DOC. Did you receive that as well?
I've got the whole thing in the self extracting archive you passed on to
Robert Williams. I'll make sure the whole lot is available with approriate
citation and a link back to your site.
>I'll give your web site a visit. Thank you.
I'll add your contribution to the site soon, probably this weekend, as well
as the solution to ReMines "problem". Thank you very much for your time.
PS. ALthough your program runs well on my lab 486, when I try and run it on
the office Pentium II I get
"runtime error 200 at 019A:0091" any ideas about this?
Cheers! Ian
The problem he reported in the PS was apparently an overflow error in the Turbo Pascal startup code, probably in a timer calibration loop, because PCs had gotten too fast. I was able to find a patch for it and fixed it. That's covered in the first section of my MONKEY page, Development History and Issues.
Again, that is at cre-ev.dwise1.net/monkey.html.
Edited by dwise1, : Changed subtitle

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 Message 35 by CRR, posted 06-26-2017 7:17 PM CRR has replied

Replies to this message:
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CRR
Member (Idle past 2242 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 39 of 252 (813354)
06-26-2017 10:41 PM
Reply to: Message 38 by dwise1
06-26-2017 9:32 PM


Re: Everybody's got something to hide, except for me and my MONKEY
Thanks for that information. It's pretty much what I inferred from the page in TO.
Neither WEASEL nor MONKEY were ever intended to simulate realistic biological populations. Again, it is not a simulation of evolution! If anyone says otherwise I refer them to you.
Edited by CRR, : edit

This message is a reply to:
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dwise1
Member
Posts: 5930
Joined: 05-02-2006
Member Rating: 5.8


Message 40 of 252 (813371)
06-27-2017 12:56 AM
Reply to: Message 39 by CRR
06-26-2017 10:41 PM


Re: Everybody's got something to hide, except for me and my MONKEY
But will you now read the source and see what it's really about?

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CRR
Member (Idle past 2242 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 41 of 252 (813372)
06-27-2017 1:39 AM
Reply to: Message 40 by dwise1
06-27-2017 12:56 AM


Re: Everybody's got something to hide, except for me and my MONKEY
No need. It was only that TO mentioned it and it has now been shown to not be relevant.

This message is a reply to:
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dwise1
Member
Posts: 5930
Joined: 05-02-2006
Member Rating: 5.8


(1)
Message 42 of 252 (813374)
06-27-2017 1:58 AM
Reply to: Message 41 by CRR
06-27-2017 1:39 AM


Re: Everybody's got something to hide, except for me and my MONKEY
But single-step selection versus cumulative selection is very relevant. As such, it needs to be examined.
I forget. Were you one of those deluded creationists who tried to force single-step selection upon evolution with a terminally false creationist probability argument? Sorry, but it's hard to keep you all apart.

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Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.6


Message 43 of 252 (813416)
06-27-2017 11:24 AM
Reply to: Message 35 by CRR
06-26-2017 7:17 PM


Re: advantageous mutations
CRR writes:
--Many genes would have been linked with genes that are selected and thus would have hitchhiked with them to fixation.
That would actually tend to limit genetic drift to that of actively selected genes. Since ReMine is talking about 1670 beneficial mutations with a much smaller number being in progress at any time this is not going to be significant.
It would tend to drive more beneficial mutations to fixation, which is the whole point. Selective sweeps decrease the cost of natural selection. Much of Haldane's conclusions have been shown to be inaccurate, as Haldane himself anticipated.

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ICANT
Member
Posts: 6769
From: SSC
Joined: 03-12-2007
Member Rating: 1.5


Message 44 of 252 (813449)
06-27-2017 2:19 PM
Reply to: Message 13 by Tangle
06-16-2017 4:34 AM


Hi :Tangle
Tangle writes:
Btw, it's always useful to know with a newbie creationist, how old do you think the earth is?
A lot older than you do.
I just had to answer that question.
God Bless,

"John 5:39 (KJS) Search the scriptures; for in them ye think ye have eternal life: and they are they which testify of me."

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 Message 13 by Tangle, posted 06-16-2017 4:34 AM Tangle has replied

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 Message 45 by Tangle, posted 06-27-2017 4:17 PM ICANT has not replied

  
Tangle
Member
Posts: 9489
From: UK
Joined: 10-07-2011
Member Rating: 4.9


(1)
Message 45 of 252 (813456)
06-27-2017 4:17 PM
Reply to: Message 44 by ICANT
06-27-2017 2:19 PM


ICANT writes:
A lot older than you do.
I remember, your the one that thinks it's trillions of years old!
So we have Faith at 6,000 years, CRR at the normal 3.4bn (I think) Dredge says somewhere between 6,000 and billions of years, and you at trillions.
It as confusing as remembering all your different and contradictory religious beliefs. You should really have it in your signatures so we know what versions we arguing against.
And my question about the Mountains of Ararat being where the Ark set down but you claiming they were only formed 100 years later?

Je suis Charlie. Je suis Ahmed. Je suis Juif. Je suis Parisien. I am Mancunian. I am Brum. I am London.
"Life, don't talk to me about life" - Marvin the Paranoid Android
"Science adjusts it's views based on what's observed.
Faith is the denial of observation so that Belief can be preserved."
- Tim Minchin, in his beat poem, Storm.

This message is a reply to:
 Message 44 by ICANT, posted 06-27-2017 2:19 PM ICANT has not replied

Replies to this message:
 Message 46 by CRR, posted 06-28-2017 12:11 AM Tangle has replied

  
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