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How would Noah's Ark accomodate mitochondrial DNA diversity? How would Noah's Ark accomodate mitochondrial DNA diversity?

01-29-2014 , 04:18 PM
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Originally Posted by zumby
I can't be arsed rewriting Bayes theorem again, but the logic here is to compare how likely it is that we would see evolution from simple cells to complex multi-cellular life if theism is true or P(E|T). Well, if theism is true then there is an all-powerful being who could make complex life in many different ways. God is unlimited, and his ways are mysterious. So there is an extremely wide probability space for ways that complex life could be brought into being if T is true, of which E is just one (or perhaps a small subset). Therefore P(E|T) is very small (reasonably it's approaching infinity to 1 but I don't need infinity to make the point). A theist should object to this unless they want to say that god had limited options when he decide dto create life.
If I were a theist, I'd object to it on the grounds that evolution is the best method - god by nature will choose the best method. P(E|T)=1 but his proclivity to choose E isn't a limitation but a sign of his cleverness.
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What about ~T (atheism)? Well, if ~T is true then as far as we know evolution is the only way to get complex life. Therefore P(E|~T) is high. Again, a theist should object here unless they want to say that it's easy to get complex life on the assumption of atheism (which they don't want to say).
I dont think this is right. They just have to say that there are many possible mechanisms for explaining complex life - those mechanisms don't all have to hold in reality. They're not therefore beholden to the view that its actually easy to create life (the historical method of complex life arising might actually be randomisation, for example. A high probability of randomisation as the method doesn't imply that there's a high probability of life arising).
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If we started from perfect ignorance about P(T) we might say that it's prior probability is 0.5. Some argue about this - that it should be much lower - but I'll be generous. If we plug in the rough numbers our prior probability of theism goes down from 0.5 to something much smaller (depending on exactly how close to 1 and 0 we put P(E|T) and P(E|~T).

Therefore, the fact that we evolution has happened reduces the probability that god exists. Of course, this doesn't show that evolution is logically incompatible with theism. But by picking one of the near-infinite ways god could produce multi-cellular life (and the one that is predicted/retrodicted on the assumption of atheism) we should see that evolution increases confidence in atheism and decreases it in theism.

For the record, by applying the same reasoning, I think that NDEs are evidence for theism... NDEs are better predicted by theism than atheism. That might change as we learn more about what is happening in these experiences, but it counts in theisms favour imo.

The reason I am secure in my atheism is that aside from NDEs, virtually everything about this universe is better predicted by atheism than theism. E.g. the problem of suffering (not logically incompatible, but better predicted by atheism via Malthus etc), the existence of large, vulnerable brains (don't need them if we gots soul), failure of intercessory prayer, etc etc.
I reject these kinds of probabilistic arguments, since they're just indicative of our current state of knowledge - depending on which clues we've gleaned, the denominator in our Bayesian calculations can vary enormously. I'd be inclined to adopt them if forced to take a view on some issue, but when it comes to theism (or most philosophical questions) I think there's a trap of feeling confident in ones positions thanks to maths - maths based solely on the limits of our knowledge at any given time.

Last edited by bunny; 01-29-2014 at 04:24 PM.
How would Noah's Ark accomodate mitochondrial DNA diversity? Quote
01-29-2014 , 04:43 PM
Quote:
Originally Posted by zumby
What about ~T (atheism)? Well, if ~T is true then as far as we know evolution is the only way to get complex life. Therefore P(E|~T) is high.
As another, perhaps clearer illustration of my aversion to this kind of argument. If we take this as true, imagine I now invent a brilliant new methodology of life creation. If what you say here is true, my invention of that has just made atheism less likely as P(E|~T) is now a little smaller.
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01-29-2014 , 04:44 PM
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I reject these kinds of probabilistic arguments, since they're just indicative of our current state of knowledge - depending on which clues we've gleaned, the denominator in our Bayesian calculations can vary enormously. I'd be inclined to adopt them if forced to take a view on some issue, but when it comes to theism (or most philosophical questions) I think there's a trap of feeling confident in ones positions thanks to maths - maths based solely on the limits of our knowledge at any given time.
I agree with this. I realize Zumby is a fan of Bayesian calculations but I find Bayesian calculations unhelpful in terms of philosophy. I am not the most mathematically oriented though, so there is that too.
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01-29-2014 , 06:23 PM
If we're going to go tangentially back and forth on qualify of evidence, the most resounding evidence for evolution is classical Mendellian genetics and its prediction on the nature of hereditary mechanisms, affirmed by Watson & Crick's seminal research and the discovery of DNA.

It is perhaps one of the most outstanding predictions of science in the last millennia. The only reason we're not awed by it, is because it is outstanding to such a degree that these days the relationship is seen as trivial. And ironically, there is no higher praise in science than that.
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01-29-2014 , 06:35 PM
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Originally Posted by LEMONZEST
I agree with this. I realize Zumby is a fan of Bayesian calculations but I find Bayesian calculations unhelpful in terms of philosophy. I am not the most mathematically oriented though, so there is that too.
I'll do this one first as it's easy. Notice that, despite frequently debating moral philosophy, I don't make Bayesian arguments about morality. If you look moderately closely, I make Bayesian arguments when the subject is about what is likely, or expected, or that X is evidence for Y. That is the proper domain of probability. The problem I have with NotReady (and you by extension) is that he wants to make arguments about what is more likely (i.e. smack dab in the domain of probability) but gets defensive when I show him that his use of probabilistic language does not line up with the math that is supposed to underpin it.
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01-29-2014 , 06:41 PM
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Originally Posted by bunny
As another, perhaps clearer illustration of my aversion to this kind of argument. If we take this as true, imagine I now invent a brilliant new methodology of life creation. If what you say here is true, my invention of that has just made atheism less likely as P(E|~T) is now a little smaller.
This is fine. Isn't it clear that, if we had hundreds of plausible and well-supported theories for the diversity of life, the ToE would not - in itself - be compelling evidence for atheism? Regardless, I find this sort of objection distasteful. I don't think we should dismiss a highly influential mathematical theorem just because it might, counter-factually, provide a framework in which theism could provide evidence. Start thinking of beliefs as degrees of confidence that can move around.
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01-29-2014 , 06:42 PM
Quote:
Originally Posted by bunny
As I understand it, the issue of timescale is a genuine puzzle and one being worked on.
There is no puzzle - what are you referring to?
How would Noah's Ark accomodate mitochondrial DNA diversity? Quote
01-29-2014 , 06:52 PM
Quote:
Originally Posted by bunny
If I were a theist, I'd object to it on the grounds that evolution is the best method - god by nature will choose the best method. P(E|T)=1 but his proclivity to choose E isn't a limitation but a sign of his cleverness.
Angels put a bit of a spanner in that argument.

But yeah, you can ad hoc your way out of anything, if that's your bag.

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I dont think this is right. They just have to say that there are many possible mechanisms for explaining complex life - those mechanisms don't all have to hold in reality. They're not therefore beholden to the view that its actually easy to create life (the historical method of complex life arising might actually be randomisation, for example. A high probability of randomisation as the method doesn't imply that there's a high probability of life arising).
A hypothetical theist might say this, but IRL theists don't, so I don't know if this is worth following through. Remember that my original complaint here was the tension that exists when a theist holds both that the non-existence of a mechanism supports theism, but the existence of a mechanism does not correspondingly reduce support for theism. Inventing new theists is kinda distracting.

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I reject these kinds of probabilistic arguments, since they're just indicative of our current state of knowledge - depending on which clues we've gleaned, the denominator in our Bayesian calculations can vary enormously. I'd be inclined to adopt them if forced to take a view on some issue, but when it comes to theism (or most philosophical questions) I think there's a trap of feeling confident in ones positions thanks to maths - maths based solely on the limits of our knowledge at any given time.

Probability IS just states of knowledge. If I flip a coin and ask you to tell me the probability that it lands heads you will say it's 50/50. But if I make a robot that can look at a coin before it is flipped, crunch some numbers and predict heads or tails with 80% accuracy... what is the REAL probability? The is no REAL probability - probability is a property of our minds (specifically our knowledge/ignorance) not an intrinsic property of the coin or coin-flip.

(For those of a deterministic bent, given only one possible future, what is the probability that the next coin I flip is heads?)
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01-29-2014 , 07:04 PM
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Originally Posted by bunny
I'm certainly no defender of Darwinism (I don't actually know what that is). As I understand it, the issue of timescale is a genuine puzzle and one being worked on. I haven't seen anyone suggest its insoluble though.
Neo-Darwinism is mutation+natural selection=macroevolution.

Nothing is proven 100% by finite, timebound, sinful man.
How would Noah's Ark accomodate mitochondrial DNA diversity? Quote
01-29-2014 , 07:13 PM
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Originally Posted by zumby
Probability IS just states of knowledge.

even in QM?
How would Noah's Ark accomodate mitochondrial DNA diversity? Quote
01-29-2014 , 07:23 PM
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Originally Posted by NeueRegel
even in QM?
Not my field, but to my limited knowledge, it depends somewhat on which interpretation of QM you go with.

Last edited by zumby; 01-29-2014 at 07:29 PM. Reason: kiss
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01-29-2014 , 07:47 PM
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Originally Posted by zumby
Not my field, but to my limited knowledge, it depends somewhat on which interpretation of QM you go with.

cool, I just asked because I've been reading about Quantum Bayesianism recently and so far haven't been able to make much sense of it as an interpretation.
How would Noah's Ark accomodate mitochondrial DNA diversity? Quote
01-29-2014 , 08:13 PM
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Originally Posted by NotReady
Neo-Darwinism is mutation+natural selection=macroevolution.
What is old-Darwinism?
How would Noah's Ark accomodate mitochondrial DNA diversity? Quote
01-29-2014 , 08:49 PM
Quote:
Originally Posted by zumby
There is no puzzle - what are you referring to?
As I understand it, there is a genuine problem with explaining the diversification we see using the processes we know about in the timescales available.

As I said - I havent heard that used to suggest that "evolution" is wrong, but more likely that there are other currently unknown processes at work which generate large-scale changes more rapidly than current models predict (epigenetics and the recent about-face on "junk" DNA, as a couple of examples).

The guy who explained it to me (who is a geneticist, but was dumbing it down) essentially said that the trouble with this 'big picture stuff' is that it's difficult to research and not terribly interesting. The only people who are really keen about it are the people looking to deny evolution.

It's similar to how scientific research on speciation is not terribly active (in comparison to other areas). The people able to do the research arent really interested in proving it happens, since it so obviously does. Go to a creationist website though and there's not really talk of anything else.

Last edited by bunny; 01-29-2014 at 08:58 PM.
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01-29-2014 , 08:51 PM
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Originally Posted by NotReady
Nothing is proven 100% by finite, timebound, sinful man.
A point of genuine difference between us.

The sum of the first n odd numbers is n-squared. Cool fact and 100% proven.
How would Noah's Ark accomodate mitochondrial DNA diversity? Quote
01-29-2014 , 08:55 PM
Quote:
Originally Posted by zumby
Angels put a bit of a spanner in that argument.

But yeah, you can ad hoc your way out of anything, if that's your bag.

A hypothetical theist might say this, but IRL theists don't, so I don't know if this is worth following through. Remember that my original complaint here was the tension that exists when a theist holds both that the non-existence of a mechanism supports theism, but the existence of a mechanism does not correspondingly reduce support for theism. Inventing new theists is kinda distracting.
I would have said this, I suspect - not sure you were here when I was advancing my own peculiar take on theism.

My first comment was that you made a good point though - I agree that you can't have your cake and eat it too. The follow up was more about probabilistic arguments in metaphysics.
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Probability IS just states of knowledge. If I flip a coin and ask you to tell me the probability that it lands heads you will say it's 50/50. But if I make a robot that can look at a coin before it is flipped, crunch some numbers and predict heads or tails with 80% accuracy... what is the REAL probability? The is no REAL probability - probability is a property of our minds (specifically our knowledge/ignorance) not an intrinsic property of the coin or coin-flip.

(For those of a deterministic bent, given only one possible future, what is the probability that the next coin I flip is heads?)
Yeah, I agree completely. This is why I think it's a poor argument when the question we're looking to answer is "What is the truth?" rather than "What is our best guess?" I think probability has its place, but not in metaphysics. As I said, I think there's a seductive tinge in that anything with numbers and calculations behind it appears to be more rigorous or certain. Ultimately a probabilistic argument that A is more likely than B might just stem from evidence for A being easier to find (or even just easier to think of).

Not really advancing a cause here - just stating my position. For future reference, I guess.

Last edited by bunny; 01-29-2014 at 09:00 PM.
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01-29-2014 , 09:50 PM
I don't think the problem, if there is one, is in the use of mathematics to model probabilities.

The idea that P(E|T) < P(E|~T) seems debatable to me, but it's not a question of the math. The assumptions involved about what theism entails are the problematic parts

Quote:
Originally Posted by zumby
God is unlimited, and his ways are mysterious. So there is an extremely wide probability space for ways that complex life could be brought into being if T is true, of which E is just one (or perhaps a small subset). Therefore P(E|T) is very small (reasonably it's approaching infinity to 1 but I don't need infinity to make the point). A theist shouldn't object to this unless they want to say that god had limited options when he decided to create life.
I feel like this argument is dubious in the same way the fine tuning argument is dubious as an argument for design. It's not clear to me that the space of possible life-giving processes is infinite or nearly so. It's not clear that the space is one of a priori logical possibility. As far as whether theists would be willing to limit God's options, there are at least a few different ways Christian theology has understood what omnipotence entails, and besides that it's not clear that that the hebrew El Shaddai or the greek Pantokrator were originally understood as omnipotence in the modern sense.

I think what I would say is that zumby is right that the truth of evolution and a lot modern scientific knowledge decreases P(T) for a pretty broad range of ideas from traditional monotheistic theology. Where I disagree is that he says it doesn't matter if there are other theologies because actual theists don't hold them. I think that dismisses the topic too easily for a couple of reasons:

1) There is more to theology than just the western Christian tradition, both in terms of other theological ideas within Christianity but also in other cultures and religions.

2) Theology doesn't have to be static, and never really has been. We can reject certain theological ideas without rejecting theism. It is (imo) a valid criticism of much of modern Christianity that it has tried too hard to defend the philosophical and theological ideas of the past rather than tackling some of these problems more open-mindedly, but it's not necessary that it always remain so, and I doubt that it will remain so.
How would Noah's Ark accomodate mitochondrial DNA diversity? Quote
01-29-2014 , 11:06 PM
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Originally Posted by NotReady
I only see two classes of evidence - fossils and genetics.

On fossils I see the same as Darwin did - the fossil record doesn't support macroevolution. Most evolutionists tell us the reason the fossil record is weak is because fossils are hard to make - but then, that admits the fossil record is weak.
I disagree quite strongly. The fossil record all fits precisely what we'd expect to find if evolution is true.

When creationists ask why so much is missing, the answer is because fossils are rare. But this is stating why the fossil record isn't even stronger and not why it is weak.

The fossil record also sets up very easy standards for disproof of evolution. Find me a pre-cambrian rabbit.

We know rabbits came from somewhere. And we don't find them before a certain point. What you call "macroevolution" therefore very much explains the appearance of rabbits only after that certain point.

Now you can replace rabbits with any of a vast number of modern species. And you only need to present one.
How would Noah's Ark accomodate mitochondrial DNA diversity? Quote
01-30-2014 , 12:52 AM
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Originally Posted by Bladesman87
Find me a pre-cambrian rabbit.
Find me all the pre-cambrian transitional fossils that led to the cambrian explosion, not to mention all the other explosions.
How would Noah's Ark accomodate mitochondrial DNA diversity? Quote
01-30-2014 , 05:26 AM
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Originally Posted by NotReady
Find me all the pre-cambrian transitional fossils that led to the cambrian explosion,
Is this a joke?
How would Noah's Ark accomodate mitochondrial DNA diversity? Quote
01-30-2014 , 07:42 AM
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Originally Posted by bunny
I would have said this, I suspect - not sure you were here when I was advancing my own peculiar take on theism.
My criticism was directed at NotReady's beliefs, not bunny's former beliefs.

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My first comment was that you made a good point though - I agree that you can't have your cake and eat it too. The follow up was more about probabilistic arguments in metaphysics.

Yeah, I agree completely. This is why I think it's a poor argument when the question we're looking to answer is "What is the truth?" rather than "What is our best guess?" I think probability has its place, but not in metaphysics. As I said, I think there's a seductive tinge in that anything with numbers and calculations behind it appears to be more rigorous or certain. Ultimately a probabilistic argument that A is more likely than B might just stem from evidence for A being easier to find (or even just easier to think of).

Not really advancing a cause here - just stating my position. For future reference, I guess.
Who is talking about The Truth or metaphysics here? My point is that questions of whether something is likely or unlikely are probabilistic and need to be justified by probability theory. Imagine this conversation between two friends:

Fiver: There are more republicans in the senate than democrats.
Keehar: Wait a minute, I've got the figures here and there are 53 democrats and 47 republicans. 53 > 47, so you are wrong.
Fiver: Ah, but you see, this is a political matter, not a mathematical matter. I've very skeptical about applying mathematics to questions of politics. For sure, deciding whether there are more republicans or democrats by mathematics might make us feel more secure in our assertions, but political truth is complex. The claim that the are more republicans than democrats is just a political claim, not a mathematical claim.
Keehar: Oh you.

Similarly, just because something is about god doesn't mean it's metaphysical. There ARE metaphysical arguments for the existence of god, but some arguments for the existence of god a) put god in the role of a scientific theory... explaining some set of observations... and therefore are empirical in nature b) appeal to god being more likely to explain some observations.. and therefore have a probabilistic component that can be evaluated using math.

Take these two problems together, it kinda seems like you are saying that "if you were addressing a different kind of theism, and addressing a different type issue, then your argument wouldn't work". Sure, but who cares?
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01-30-2014 , 07:45 AM
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Originally Posted by well named
I don't think the problem, if there is one, is in the use of mathematics to model probabilities.

The idea that P(E|T) < P(E|~T) seems debatable to me, but it's not a question of the math. The assumptions involved about what theism entails are the problematic parts


I feel like this argument is dubious in the same way the fine tuning argument is dubious as an argument for design. It's not clear to me that the space of possible life-giving processes is infinite or nearly so. It's not clear that the space is one of a priori logical possibility. As far as whether theists would be willing to limit God's options, there are at least a few different ways Christian theology has understood what omnipotence entails, and besides that it's not clear that that the hebrew El Shaddai or the greek Pantokrator were originally understood as omnipotence in the modern sense.

I think what I would say is that zumby is right that the truth of evolution and a lot modern scientific knowledge decreases P(T) for a pretty broad range of ideas from traditional monotheistic theology. Where I disagree is that he says it doesn't matter if there are other theologies because actual theists don't hold them. I think that dismisses the topic too easily for a couple of reasons:

1) There is more to theology than just the western Christian tradition, both in terms of other theological ideas within Christianity but also in other cultures and religions.

2) Theology doesn't have to be static, and never really has been. We can reject certain theological ideas without rejecting theism. It is (imo) a valid criticism of much of modern Christianity that it has tried too hard to defend the philosophical and theological ideas of the past rather than tackling some of these problems more open-mindedly, but it's not necessary that it always remain so, and I doubt that it will remain so.
What theism entails, when I'm addressing NotReady, is the particular theism that he/WLC/Alvin Plantinga subscribe to. For a trivial counter-example, I don't think that dereds 'theism' is touched by this argument.
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01-30-2014 , 08:04 AM
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Originally Posted by bunny
As I understand it, there is a genuine problem with explaining the diversification we see using the processes we know about in the timescales available.
There isn't.

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As I said - I havent heard that used to suggest that "evolution" is wrong, but more likely that there are other currently unknown processes at work which generate large-scale changes more rapidly than current models predict (epigenetics and the recent about-face on "junk" DNA, as a couple of examples).
There's so much wrong with this it's hard to know where to start. First off, yes there are processes identified in the last few decades that can 'speed up' evolution. But these aren't 'unknown processes'. A contemporary evo 101 course will include PE, epigenetics etc. And none of this even remotely supports the argument that there is not enough time, but quite the opposite... as you said, these processes allow for 'quicker' evolution! Creationists claim that there was not enough time for evolution.. how you think that processes that explain 'fast' evolution are in any (however small) way helpful to this argument completely baffles me.

No serious scientist thinks there was not enough time. It's just not an issue, and hasn't been for over a hundred years.

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The guy who explained it to me (who is a geneticist, but was dumbing it down) essentially said that the trouble with this 'big picture stuff' is that it's difficult to research and not terribly interesting. The only people who are really keen about it are the people looking to deny evolution.
OK

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It's similar to how scientific research on speciation is not terribly active (in comparison to other areas). The people able to do the research arent really interested in proving it happens, since it so obviously does. Go to a creationist website though and there's not really talk of anything else.
Well I agree that no-one is trying to work out if speciation happens because LDO, but it's an active area of research in general. A quick search on Mendeley (which is far from exhaustive) throws up nearly a thousand papers on speciation published since 2013. For comparison, there were half as many papers published on epigenetics in the same time period.
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01-30-2014 , 08:32 AM
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Originally Posted by zumby
There's so much wrong with this it's hard to know where to start.
I'd suggest understanding it first, before dismissing it. Granted I'm not terribly clear when i post, but I'm no fool.
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First off, yes there are processes identified in the last few decades that can 'speed up' evolution. But these aren't 'unknown processes'. A contemporary evo 101 course will include PE, epigenetics etc. And none of this even remotely supports the argument that there is not enough time, but quite the opposite... as you said, these processes allow for 'quicker' evolution! Creationists claim that there was not enough time for evolution.. how you think that processes that explain 'fast' evolution are in any (however small) way helpful to this argument completely baffles me.
I don't. I was pointing out some (comparatively recent) examples where our understanding of evolution had broadened beyond "random mutations happen and some are advantageous". My claim (parroted, not researched) was that there used to be a big puzzle and that these recent advances have helped explain it.

Nonetheless, the processes we are currently aware of are still insufficient. The conclusion being we don't fully understand them or there are some we haven't discovered yet.
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No serious scientist thinks there was not enough time. It's just not an issue, and hasn't been for over a hundred years.
That's why I made the comment "As I said - I havent heard that used to suggest that "evolution" is wrong".
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01-30-2014 , 08:35 AM
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Originally Posted by zumby
My criticism was directed at NotReady's beliefs, not bunny's former beliefs.
"A hypothetical theist might say this, but IRL theists don't, so I don't know if this is worth following through"

Sounded more general than just NotReady, but okay. I think it's a fair criticism of NotReady's position.

Last edited by bunny; 01-30-2014 at 08:42 AM.
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