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Author Topic:   Reduction of Alleles by Natural Selection (Faith and ZenMonkey Only)
Faith
Member
Posts: 25583
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.0


Message 16 of 87 (553593)
04-04-2010 2:40 AM
Reply to: Message 1 by Blue Jay
04-01-2010 4:59 PM


Keep forgetting to ask: what is your science, Bluejay?
This message is a reply to:
 Message 1 by Blue Jay, posted 04-01-2010 4:59 PM Blue Jay has responded

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Blue Jay
Member (Idle past 165 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 17 of 87 (553619)
04-04-2010 9:12 AM
Reply to: Message 16 by Faith
04-04-2010 2:40 AM


Hi, Faith.

I'm currently a doctoral student in an entomology program. Specifically, I'm work in spider ecology.


-Bluejay (a.k.a. Mantis, Thylacosmilus)

Darwin loves you.


This message is a reply to:
 Message 16 by Faith, posted 04-04-2010 2:40 AM Faith has not yet responded

  
Blue Jay
Member (Idle past 165 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 18 of 87 (553630)
04-04-2010 11:44 AM
Reply to: Message 14 by Faith
04-04-2010 12:29 AM


Re: The crux
Hi, Faith.

Faith writes:

Its size. Its much greater numbers...

... The smaller the population the more dramatic and faster the effects; if the population is pretty good sized they will still operate but not as fast or dramatically.

That's what I thought. However, this makes the situation into a game of numbers, a math problem, to which you have strenuously objected all along.

You seem to accept that numbers and rates of change will have something to do with the problem, but you wonít accept any pro-evolution arguments that have anything to do with rates. Then, when you make comments like this---

Faith writes:

I don't deny that there may be some mutations but I really haven't seen any evidence for them -- the whole idea that mutations are the source of alleles is strictly an assumption based on evolutionary theory...

---it comes off as if youíre just arbitrarily choosing what variables can and canít be included.

I have twice referenced a paper that found approximately 60 new mutations in the genomes of two human children. If we assume 1-2% of the genome is coding DNA (i.e. genes), this means we should expect 1-2% x 60 = 0.6 new alleles per individual birth (this is genome-wide).

Why is this not evidence for mutations?
Why should mutations be simply left out of the model?

-----

Faith writes:

I'm still describing the same situation of a relatively small population which is allowing the expression of previously unexpressed alleles and new combinations.

And, in the scenario you're addressing, this makes perfect sense. But, the evidence I have presented suggests that reality does not conform to the scenario you want to address. So, naturally, I have been trying to convince you that you should address a different scenario from the one you want to address.


-Bluejay (a.k.a. Mantis, Thylacosmilus)

Darwin loves you.


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Blue Jay
Member (Idle past 165 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 19 of 87 (553633)
04-04-2010 12:02 PM
Reply to: Message 10 by Faith
04-03-2010 11:23 PM


The Title
Hi, Faith.

Faith writes:

Seems to me it's six of one and half a dozen of the other.

So, why did you make such a big deal about the title, then?


-Bluejay (a.k.a. Mantis, Thylacosmilus)

Darwin loves you.


This message is a reply to:
 Message 10 by Faith, posted 04-03-2010 11:23 PM Faith has responded

Replies to this message:
 Message 21 by Faith, posted 04-04-2010 1:54 PM Blue Jay has responded

  
Admin
Director
Posts: 12516
From: EvC Forum
Joined: 06-14-2002
Member Rating: 2.9


Message 20 of 87 (553644)
04-04-2010 1:22 PM
Reply to: Message 18 by Blue Jay
04-04-2010 11:44 AM


Re: The crux
Bluejay writes:

I have twice referenced a paper that found approximately 60 new mutations in the genomes of two human children. If we assume 1-2% of the genome is coding DNA (i.e. genes), this means we should expect 1-2% x 60 = 0.6 new alleles per individual birth (this is genome-wide).

Just wanted to clarify how the math works.

If the 60 mutations are single nucleotide mistakes that occur randomly throughout an average individual's genome, then with 3 billion nucleotides that's a mutation rate of 2 x 10-8. If 1 to 2 x 10-2 of the genome is coding (i.e., 1% to 2%) and the number of genes in the human genome is 30,000, then one could reasonably expect the number of genes with new alleles to be around 1 most of the time, because the odds for one of those mutations occurring in an actual gene is .002% to .004%, times 30,000 genes, which is 0.6 to 1.2 mutations (which are new alleles) per individual.

There are about 130 million babies born every year, and so if there's approximately one new allele per individual then on average the human race produces around 130 million new alleles every year. Some number of those would be duplicates, but getting in the ballpark statistically on that figure would not be a simple calculation.

If a small group of a hundred individuals were to become trapped on an island then they would have around 1 or 2 babies per year (I'm assuming same birth rate as the world), which is 1 or two new alleles per year.

The question you two are currently discussing is how this rate of increase in alleles in this small population compares with it's rate of loss. The death rate in the world today is only about 40% of the birth rate, so barring catastrophe the population size will increase.


--Percy
EvC Forum Director

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Faith
Member
Posts: 25583
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.0


(1)
Message 21 of 87 (553649)
04-04-2010 1:54 PM
Reply to: Message 19 by Blue Jay
04-04-2010 12:02 PM


Re: The Title /
Seems to me it's six of one and half a dozen of the other.

So, why did you make such a big deal about the title, then?

Because what I'm trying to do is make a distinction between the observed level of phenotypic change, which LOOKS additive (although in actual fact it is also reduced), and the unobserved level of genotypic change which is reduced during the processes of population splitting that lead to speciation. Evolutionists look at the new phenotypes that emerge and call that evolution (which it is) and especially if it goes as far as speciation, without noticing the corresponding reduction in alleles that has to happen to bring out the new phenotypes.

If you describe this as reducing traits you obscure the whole point that to the eye the traits are proliferating and evolving and forming new species -- which is why they are always pointed to as evidence for evolution. And this IS evolution, it is the essence of evolution.

But the underlying genetic situation is not also proliferating, it is reducing.

Yes, again, literally the traits are reducing too. That is, there are FEWER traits possible in the new populations just as there are fewer alleles available, but since they are emerging to characterize the population they APPEAR to be increasing.

This is tricky to get said but it is of the essence of my argument. What LOOKS like evolution because you're getting new variations, lots of observable change, is entirely the effect of restricting the gene pool. NUMBERS of traits are also reduced in this restricted gene pool, while the EXPRESSION of traits in the overall collection of populations based on the entire gene pool for that species is increasing. And this is what evolutionists take account of in their descriptions of evolution while overlooking the actual literal reduction that's going on.

Time and time again I've read evolutionist accounts of evolution that describe only the surface changes. Dawkins goes on and on about this or that wonderful adaptation as if new adaptations and variations could just endlessly increase out to infinity without ever once considering the underlying genetic restriction that has to have taken place for that adaptation to emerge.

==================
The following was my first answer to this post and although it just repeats the same thing in somewhat different words I'm going to leave it here for now because it may add something to the concept I'm trying to get across:

Big deal out of the title? I'm trying to prove that as traits become expressed as the defining character of new populations the genetic diversity of that population is reduced.

Traits are "reduced" only in the sense that when their alleles are removed from the population they have disappeared as possible expressions for that population, but with respect to the traits exhibited in the former population they are new and different, they are not reduced, you are getting change, you are getting new phenotypes, you are getting evolution.

The effect is additive on the surface because if you add them to the traits of the former population you can count a lot of different types of salamanders for the total salamander gene pool, and between the two populations there are of course the corresponding underlying genetics for ALL the traits as well, but different alleles are getting expressed in the different context. In the new population "new" alleles are getting expressed with respect to the first population because some from the first have been suppressed or eliminated to allow the "new" ones to emerge and get expressed.

You really still don't quite get what I'm trying to get at. Not that I blame you but I have to keep bringing us back to it.

Obviously I'm trying to say something that evolutionists don't believe and don't address and really, don't even think about. Naturally you keep trying to take me back to what evolutionists think. If you can prove I'm wrong that's one thing, but if the discussion is going to make sense you really do have to get what I'm trying to say.

========================
Literally both alleles and traits are decreasing as new variations emerge.

Dynamically (just thought of that word as possibly descriptive here) while you are adding traits to traits as you get new breeds or variations, what is REALLY going on is this overall reduction and loss of diversity. Yes, literally also loss of trait diversity too in the new breed, but when we just look at the increase in overall variations for the total population we add it all together and call it an increase, which it is for the TOTAL population.

================================
ABE: Maybe I should say the EMERGENT or EXPRESSED TRAITS are increasing in these daughter populations while the alleles are being reduced AND the actual number of traits is reduced?

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.


This message is a reply to:
 Message 19 by Blue Jay, posted 04-04-2010 12:02 PM Blue Jay has responded

Replies to this message:
 Message 22 by Faith, posted 04-04-2010 2:33 PM Faith has not yet responded
 Message 24 by Blue Jay, posted 04-04-2010 10:57 PM Faith has responded

    
Faith
Member
Posts: 25583
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.0


Message 22 of 87 (553650)
04-04-2010 2:33 PM
Reply to: Message 21 by Faith
04-04-2010 1:54 PM


Re: The Title /
Sorry to keep going on and on but I want to add something to my last post in a separate post.

Time and time again I've read evolutionist accounts of evolution that describe only the surface changes. Dawkins goes on and on about this or that wonderful adaptation as if new adaptations and variations could just endlessly increase out to infinity without ever once considering the underlying genetic restriction that has to have taken place for that adaptation to emerge.

This is because he thinks it was the addition of new alleles by mutation that created this adaptation.

This assumption is probably the core of the debate really and why you all want to tell me that mutations are what I'm overlooking.

So back before this new adaptation emerged, in the previous population of the species, put your mutations for this adaptation into the picture and then apply selection pressure so that it starts to spread in the population, Pink Sasquatch's longer flycatching tongue for her frog way back in the original thread perhaps, and then notice:

As the longer tongue comes to characterize the population, you are losing all the other kinds of tongues, the shorter tongues, AND the genetic substrate for them -- at least you are reducing their number (or more accurately, their proportion) in the total population.

The mutation is getting selected but exactly the same processes of reduction are occurring that I've been describing.

The shorter tongues may remain latent in the population -- I'm not sure how this works genetically -- dominant and recessive forms at least? -- but it's certainly what happens in those moths that turn from light to dark according to their background -- they never speciated or evolved into one or the other type, they continue to be able to go back and forth between the two types. And that could happen with the frog tongues too. In that case you aren't getting an established or fixed variation, and you aren't getting evolution if you mean going from one to another variation without end.

But if you do get a fixed variation, or speciation, a truly new frog type with this longer tongue that can't interbreed with its former family members, then you've not only lost all those shorter tongues forever in the new frog species but all the alleles for them. You've lost the genetic diversity needed to go on evolving.

And if natural selection works on traits, then of course you've lost the trait diversity too. Bluejay has made me aware that I need to take this into account. It IS true that the traits are ALSO being reduced as the new one becomes fixed. I was taking that for granted but it's just as true as that alleles are being reduced. Also, it's no doubt right to say that natural selection works on the traits as well as the genes. I've been focusing on the surface fact of an apparent increase in traits all added together for the total species, because that's where evolutionist descriptions focus, so I emphasize that it costs genetically for new traits to emerge. But the new trait is just as much the product of a reduced pool of traits as its allele is the product of the reduced pool of alleles.

I see that Bluejay wants to answer my claim that a large sized population isn't evolving according to this progression of processes I'm describing by bringing in mathematics. That isn't going to fly with a nonmathematical brain like mine, and I would simply like to point out that Darwin also confessed to being mathematically challenged so hold the derision please.

The size of the population IS relevant. Population geneticists write quite a bit about how genetic drift acts more slowly in large populations, and in fact everything that brings about new species acts more slowly if at all.

But I'll try to get what Bluejay is saying.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.


This message is a reply to:
 Message 21 by Faith, posted 04-04-2010 1:54 PM Faith has not yet responded

Replies to this message:
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Blue Jay
Member (Idle past 165 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


(1)
Message 23 of 87 (553743)
04-04-2010 10:27 PM
Reply to: Message 22 by Faith
04-04-2010 2:33 PM


Re: The Title /
Hi, Faith.

Faith writes:

Sorry to keep going on and on but I want to add something to my last post in a separate post.

I've got no objection to your debate style or posting style at all. I won't be able to (or interested in) responding to everything you post, but I have read essentially all of it. Go ahead and keep posting however frequently and however much you want to: I'm sure you and I aren't the only ones reading this.

My next response is nearly complete: it's taken me all day because I've had to work around several church meetings, Easter celebration with visiting family members, entertaining the baby and putting him to bed, and cleaning up afterwards.

I think I'm almost ready. Thanks for your patience.


-Bluejay (a.k.a. Mantis, Thylacosmilus)

Darwin loves you.


This message is a reply to:
 Message 22 by Faith, posted 04-04-2010 2:33 PM Faith has not yet responded

  
Blue Jay
Member (Idle past 165 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 24 of 87 (553752)
04-04-2010 10:57 PM
Reply to: Message 21 by Faith
04-04-2010 1:54 PM


Faith and the Seals
Hi, Faith.

Here, I'm going to deviate a bit from my pattern so far. I'm not going to respond directly to any of the points you've been saying: I'm going to present a detailed counterpoint, starting with this prompt:

Faith writes:

You really still don't quite get what I'm trying to get at.

I understood exactly what you said the first time you said it. In fact, your argument is really an old concept, dating to the 1950ís in genetics, and is a concept I learned about in my undergraduate genetics courses. There is a name for it: the Founder Effect.

It generally combines three basic, interrelated evolutionary concepts: (1) genetic bottlenecks; (2) allopatric speciation (i.e., speciation by physical isolation); and (3) genetic drift.

It is a well-documented and well-known phenomenon. You identified several key examples of it (seals, cheetahs, etc.), and nobody is disputing that it happens, that it can have major consequences on a population, or that it reduces genetic diversity in that population.

Once again, all that is being disputed is the universality of your argument. I personally dispute the universality of your argument on two fronts: (1) the time it takes to kill a species after it passes through a bottleneck; and (2) the well-documented evidence for the occurrence of diversity input into the system (i.e. mutations).

-----

As an example, letís consider the Northern elephant seal. According to the Wiki article, they reached their low point (total population less than 1000 individuals) in the late 1800ís/early 1900ís. With the help of hunting bans, in the roughly 100 years since, their population has increased to over 100,000.

They reached a severe genetic bottleneck over a century ago, but are not extinct yet. Letís try to apply the human mutation rate to the elephant seals and see what their genetic diversity is like today (donít worry: Iím not particularly mathematically inclined, either---as you can see by my math needing to be clarified by Admin).

So, letís use 0.6-per-individual as the rate of new alleles in the population (it's friendlier to your argument than Percy's figure). Thus, we should estimate that there are approximately (100,000 individuals x 0.6 new alleles/individual) = 60,000 new alleles among the currently living elephant seals, without considering all the individuals that lived and died and mutated in the interim. If elephant seals have roughly the same number of genes as humans (22,000), that means they should average almost 3 new alleles per gene (granted, some genes will have mutated much more or much less than this, so this average may be pretty much a meaningless number).

Many of these new alleles will not be passed on to the next generation, and many others are at such low levels as to be effectively irrelevant to the current gene pool. But, with so many tens of thousands of new alleles having been introduced, what are the chances that none of them is catching on? What are the chances that none of them will alter (or have altered) the patterns of natural selection in the population?

Perhaps more to the point, how long is it going to take for this depleted gene pool to finally implode under the pressures of natural selection? All indications are that these seals are fully capable of persisting long enough to see their populationís genetic diversity return to a healthy level by means of subtle, gradual accumulation of random mutations.

So, why should we think that reduced genetic diversity is, in principle, an insurmountable obstacle in all evolutionary scenarios? It looks to me like this is far from a foregone conclusion.


-Bluejay (a.k.a. Mantis, Thylacosmilus)

Darwin loves you.


This message is a reply to:
 Message 21 by Faith, posted 04-04-2010 1:54 PM Faith has responded

Replies to this message:
 Message 25 by Faith, posted 04-05-2010 1:42 AM Blue Jay has responded

  
Faith
Member
Posts: 25583
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.0


Message 25 of 87 (553781)
04-05-2010 1:42 AM
Reply to: Message 24 by Blue Jay
04-04-2010 10:57 PM


Re: Faith and the Seals
Since mutations that actually contribute to the health of a species by making new viable alleles are an assumption imposed by the theory of evolution, it would be more convincing if you'd actually go and take DNA samples of at least 1000 of the seals to check their genetic diversity.

Do it also with each population of the salamanders of the ring populations in California and of the seagulls that ring the northern Atlantic and the chipmunks around the Sierra. Otherwise this is all hot-air theorizing as an argument.

More later.

By the way, I could have listed Founder Effect myself. It adds nothing to your argument, just gives you another label under which to say the same old thing.

But yes, that's the idea, so at least now I know you get it.

So I'll try again tomorrow.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.


This message is a reply to:
 Message 24 by Blue Jay, posted 04-04-2010 10:57 PM Blue Jay has responded

Replies to this message:
 Message 26 by Blue Jay, posted 04-05-2010 10:32 AM Faith has responded

    
Blue Jay
Member (Idle past 165 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 26 of 87 (553835)
04-05-2010 10:32 AM
Reply to: Message 25 by Faith
04-05-2010 1:42 AM


Re: Faith and the Seals
Hi, Faith.

I think the mood of the thread suddenly turned icy, and I'm pretty sure I didn't do anything to deserve it.

Why donít we slow down? Iím going to restrict myself to one post a day: maybe that will help keep the passion and frustration out of it.

Faith writes:

Since mutations that actually contribute to the health of a species by making new viable alleles are an assumption imposed by the theory of evolution...

What's to stop a beneficial mutation from happening?
The effects of a mutation on the organism have nothing to do with the mechanism that causes the mutation; so benefit or detriment cannot possibly have impacted the occurrence of the mutation.

By analogy: People can walk. But, it's an assumption imposed by evolutionary theory that people can walk to a watering hole to get water. This makes no sense!

Unless there is some mechanism that would prevent any particular nucleotide from changing to a "better" nucleotide, there is no reason to think beneficial mutations can't occur.

The only reason to propose such a thing is if you are assuming that the way things currently are is already optimal, and cannot be improved upon. My personal work in ecology tells me that to assume such would be very inappropriate: the behavior of most organisms is not particularly optimal or efficient.

-----

Faith writes:

...it would be more convincing if you'd actually go and take DNA samples of at least 1000 of the seals to check their genetic diversity.

Science learns and grows all the time.

If the people 100 years ago had had the foresight to take genetic samples back when the seals were almost extinct, maybe we could learn something about genetic bottlenecks and subsequent recoveries today. But, at that time, they werenít even aware of what function DNA performed. All we can really do is learn to do it right in the next study.

If youíd like, when I become a full professor (that will take more than 10 years, probably), I can write a grant, and you and I can go sequence elephant seal genomes together. Of course, my grant will probably get rejected, because not only is research funding for non-applied stuff getting whittled down to nothing, but I do not have, and probably never will have, the credentials to work with elephant seals or genome-sequencing technology. Sorry to disappoint you, but the best I can do is wait for seal people to do the work themselves.

But, in the meantime, Iíve already presented a paper that used modern genetic techniques to compare the whole-genome sequences of children to their parents, and it showed that 60 was a rough average for the number of mutations per individual. To my knowledge, this is the first time such an experiment has been done. It's hard, expensive work to sequence an entire genome to look for mutations, let alone to sequence the genomes of multiple individuals for comparison. Now that itís got precedent, and the tools are becoming more accessible, Iím sure we may be seeing more of it soon, and many examples of new alleles will start coming forward.

However, the only practical way to study mutations currently is to look for gross disfigurement in fruit flies or Arabidopsis plants and try to see if there is a genetic basis for the disfigurement. This is hardly conducive to assessing the rates of beneficial mutations, so it shouldnít surprise anybody that we rely on correlative field data.

But, for now, all the data we have collected suggests that there is no reason to deny the possibility of beneficial mutations, and no reason to think that genetic bottlenecks are insurmountable to biological populations. There is only data that is favorable to the possibility that the genetic diversity of a population can increase over time.

-----

Faith writes:

By the way, I could have listed Founder Effect myself. It adds nothing to your argument, just gives you another label under which to say the same old thing.

You think I did it for libel?

I did it because I saw it as the only way to get you to stop thinking you have to repost the basic description of your argument in every response. We werenít getting anywhere with you repeating the same thing over and over again; and, since Iím very interested in getting somewhere with this discussion, I had to do something that might sound a bit condescending.

I apologize for patronizing you, but how else could I have proven to you that I actually do understand your argument?


-Bluejay (a.k.a. Mantis, Thylacosmilus)

Darwin loves you.


This message is a reply to:
 Message 25 by Faith, posted 04-05-2010 1:42 AM Faith has responded

Replies to this message:
 Message 27 by Faith, posted 04-06-2010 4:51 PM Blue Jay has responded

  
Faith
Member
Posts: 25583
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.0


Message 27 of 87 (554156)
04-06-2010 4:51 PM
Reply to: Message 26 by Blue Jay
04-05-2010 10:32 AM


evidence for mutations.
Bluejay you do AND you don't understand my argument as far as I can tell. Founder Effect is OK as a general category but it restricts it in ways I try not to. Never mind, I'm still listening to the You Tube lecture by the Yale biologist and trying to find out if there are new ways for me to think this through, including what you have to say here.

I did get icy, sorry, not sure what you said, maybe something on the other thread. Maybe just feeling you're with them and they're against me and of course ultimately you are too even if you're being nice. Sorry, I'll try to keep it down.

I'll probably be dead by the time you're a professor.

What's to stop a beneficial mutation from happening?

Well, if you assume evolution, nothing, but if like me you don't, you'd have to prove that they happen at all -- any that actually form useful alleles, that is. Honestly, I haven't seen it yet. Discussions of mutations still sound awfully hypothetical, EXCEPT for the ones they know about that cause diseases -- and there are thousands of those.

Yes, I'm sure even as I ask for direct proof of genetic diversity that it's just not practical. Sequencing a genome has to be laborious and expensive. But I don't see how else a creationist is going to be able to show that the evolutionist assumptions might be wrong if it's all dependent on interpretations of "correlative field data" that is interpreted through the lens of evolution.

You talk about the 60 mutations per individual -- how did you arrive at that? You actually looked at the genomes you say. I'd really like to understand what you saw but if it's in the form of those odd-looking DNA graphs or mathematical formulas no way. What do you think of those mutations? They're all mistakes in replication? How many are going to be disease-causing or removed by selection because of being defective? Etc.

I wish it were possible to actually SEE a genome, see a chromosome, see a gene.

The effects of a mutation on the organism have nothing to do with the mechanism that causes the mutation; so benefit or detriment cannot possibly have impacted the occurrence of the mutation.

True. I think I was assuming that most detriminental alleles would be selected out, and that speciation would be built from healthy ones, but obviously genetic diseases also proliferate. I didn't think there was anything controversial about my statement.

Perhaps we do need to get into mutations in some depth because I can't help but have the assumption at the back of my head all the time, much as I try to suspend it for purposes of this discussion, that mutations are predominantly deleterious and the actual evidence for any kind of mutation that could actually power evolution is pretty much nonexistent, that the idea of such mutations is entirely hypothetical and assumed, taken for granted but not actually ever demonstrated.

This would make sense of course for anyone absolutely convinced of the theory of evolution because of COURSE such mutations MUST occur in that case, so whenever you describe any case of the emergence of a new phenotype you AUTOMATICALLY assume it's the product of a mutation. I've been trying to go along with this because I don't think it makes much difference to the point I've been trying to make, but it apparently needs to be talked through.

In fact if there ISN'T any real proof of mutations beyond the bad ones my argument is more solid anyway, so it would be good to know for sure what the situation really is.

There is only data that is favorable to the possibility that the genetic diversity of a population can increase over time.

I've seen this claimed many times. I haven't seen it actually demonstrated to be true, or even demonstrated to be the possibility you are saying it is.

If it's all from purely hypothetical mutations I'm going to remain unconvinced. If it's all from observed mutations in the genome without a clear idea of what those mutations are actually doing, I'm going to be unconvinced too and maybe that's all there is to say about it anyway since this is pretty much what you aresaying here:

However, the only practical way to study mutations currently is to look for gross disfigurement in fruit flies or Arabidopsis plants and try to see if there is a genetic basis for the disfigurement. This is hardly conducive to assessing the rates of beneficial mutations, so it shouldnít surprise anybody that we rely on correlative field data.

No, it doesn't, but isn't convincing to a creationist as the whole assumption rests on an acceptance of the theory of evolution.

If you INSIST on making mutations your argument against me, I don't see how you can do this if you can't REALLY prove they exist. Which is what I've been assuming all along anyway. So I've ALSO been trying to assume they exist for the sake of argument and trying to construct my argument around that assumption.

I have a feeling that's where it has to remain, that there isn't really any more to it, right?

I'm not sure I did your post justice. I also have in mind your previous post where you say something about studies done in the 50s that deal with the sort of observations I'm occupied with. Is there any way for me to see those, or any way for you to translate them into English so that I can grasp what they were all about? Never mind, I see you were just talking about the Founder Effect. But I have run across references to studies in population genetics that were done about that time that I've thought I should read up on. I have some sources of my own though.

In any case, I'm going back to the Yale lectures on You Tube next. If I've left anything out of my response to you, or misread anything, please put it in the next post.

Thanks.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.


This message is a reply to:
 Message 26 by Blue Jay, posted 04-05-2010 10:32 AM Blue Jay has responded

Replies to this message:
 Message 28 by Blue Jay, posted 04-06-2010 7:21 PM Faith has responded

    
Blue Jay
Member (Idle past 165 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


(1)
Message 28 of 87 (554179)
04-06-2010 7:21 PM
Reply to: Message 27 by Faith
04-06-2010 4:51 PM


Re: evidence for mutations.
Hi, Faith.

Faith writes:

I did get icy, sorry, not sure what you said, maybe something on the other thread. Maybe just feeling you're with them and they're against me and of course ultimately you are too even if you're being nice. Sorry, I'll try to keep it down.

I understand the feeling. I donít have the stamina to hold up against even a few opponents, so I admire your fortitude.

-----

Faith writes:

I'll probably be dead by the time you're a professor.

The way things are going now, I often feel like Iíll be dead by then, too.

-----

Faith writes:

You talk about the 60 mutations per individual -- how did you arrive at that?

Well, I didnít: that figure was from a recently published study ( click here for a news article written about the study).

In that study, the researchers actually sequenced the entire genomes of a husband and wife, and the genomes of their two children. They were able to identify places in the genome where the childrenís sequence differed from both parentsí genomes. Each childís genome contained about 70* places that differed from both parentsí genomes.

Thatís 70* differences (mutations) in one generation.

*The news article says 60, but the actual study says 70 (I missed this on my first time through).

-----

Faith writes:

What do you think of those mutations? They're all mistakes in replication? How many are going to be disease-causing or removed by selection because of being defective?

The paper stated that both children had two recessive genetic disorders, but does not actually state whether these were due to mutation: my feeling is that these were not related to the mutations identified. As far as I can tell (most of the paper is beyond my education), none of the mutations identified was detrimental: given that the samples were taken from living children, the mutations were obviously at least not fatal.

No data were presented on the phenotypic effects of the mutations, but, given that the children do not seem to have been adversely affected by any of these mutations, they would appear to be neutral or, at worst, very slightly deleterious, and some may even have been beneficial.

-----

Faith writes:

Well, if you assume evolution, nothing [is to stop beneficial mutations from happening], but if like me you don't, you'd have to prove that they happen at all -- any that actually form useful alleles, that is. Honestly, I haven't seen it yet. Discussions of mutations still sound awfully hypothetical, EXCEPT for the ones they know about that cause diseases -- and there are thousands of those.

There have been hundreds of scientific studies that have conclusively demonstrated that mutations happen. There is no way to realistically deny that mutations happen.

Given that, we then have to decide what constitutes a ďbeneficialĒ mutation, and why this would represent a special case of a mutation that cannot happen.

When we add to this the simple observation that the occurrence of mutations is not sensitive to the phenotypic effects that the mutation would have on the organism, I donít see how there is anything that could stop a beneficial mutation from happening.

In terms of the scientific method, the default conclusion is that beneficial mutations can and do happen. The alternative is to propose that there is a special mechanism in place that prevents mutations from happening if those mutations would have a positive effect on phenotype. Since there is no evidence for such a special mechanism, there is no reason to think that beneficial mutations are different from any other kind of mutation in terms of whether or not they can happen.

It can be extremely difficult to identify ďbeneficialĒ mutations, because ďbenefitĒ is highly context-specific. For instance, mutations have been identified that cause plants to grow taller than they otherwise would. This would be beneficial where competing plants were tall, because it would allow the plant to reach sunlight, but it would not really be useful for a plant that has little competition for sunlight.

However, many kinds of detrimental effects can be easily identified because of the obvious deformities they cause. This is the only really sure reason why we know so many more detrimental mutations than beneficial mutations.


-Bluejay (a.k.a. Mantis, Thylacosmilus)

Darwin loves you.


This message is a reply to:
 Message 27 by Faith, posted 04-06-2010 4:51 PM Faith has responded

Replies to this message:
 Message 29 by Faith, posted 04-06-2010 10:07 PM Blue Jay has responded

  
Faith
Member
Posts: 25583
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.0


Message 29 of 87 (554211)
04-06-2010 10:07 PM
Reply to: Message 28 by Blue Jay
04-06-2010 7:21 PM


Re: evidence for mutations.
-----
Faith writes:
You talk about the 60 mutations per individual -- how did you arrive at that?

Well, I didnít: that figure was from a recently published study.

Oh right, I'd seen that, thought you were saying something else, some study YOU had done. OK.

In that study, the researchers actually sequenced the entire genomes of a husband and wife, and the genomes of their two children. They were able to identify places in the genome where the childrenís sequence differed from both parentsí genomes. Each childís genome contained about 70* places that differed from both parentsí genomes.

Thatís 70* differences (mutations) in one generation.

*The news article says 60, but the actual study says 70 (I missed this on my first time through).

Faith writes:
What do you think of those mutations? They're all mistakes in replication? How many are going to be disease-causing or removed by selection because of being defective?

The paper stated that both children had two recessive genetic disorders, but does not actually state whether these were due to mutation: my feeling is that these were not related to the mutations identified. As far as I can tell (most of the paper is beyond my education), none of the mutations identified was detrimental: given that the samples were taken from living children, the mutations were obviously at least not fatal.

But it was also not clear what exactly they DID do, if anything, right? As you say next:

No data were presented on the phenotypic effects of the mutations, but, given that the children do not seem to have been adversely affected by any of these mutations, they would appear to be neutral or, at worst, very slightly deleterious, and some may even have been beneficial.

The thing here, for a creationist, is that what you know is only that there are 70 alleles whose codes have been changed with respect to the parents' genomes. (How big the changes are would be interesting to know too, it just occurred to me, that is, how many codons are affected at each locus and the effects of any differences in how many and that sort of thing.)

That is what a mutation is, of course, but from this study it doesn't appear that you know anything about them that would validate the assumption that all alleles originated with this kind of event, which IS the assumption of evolution, right? That is, you don't have any evidence that any of them code for anything in the normal range of the things that alleles code for in the making of traits.

One thing scientists apparently DO know is quite a bit about some of such changes that are responsible for genetic diseases, and I've seen references to thousands of these -- that is about all I see that is actually KNOWN about what they do. There are a few that apparently have negative effects of some sort that somehow also work out to a benefit in some area (malaria/sickle cell and another I keep forgetting). But that doesn't seem to me to be anything that could be considered a model for the kinds of changes evolution needs mutations to be.

No data were presented on the phenotypic effects of the mutations, but, given that the children do not seem to have been adversely affected by any of these mutations, they would appear to be neutral or, at worst, very slightly deleterious, and some may even have been beneficial.

Is it fair to suppose that the scientists doing this study would be planning to go on to study these same mutations to try to find out exactly what phenotypes they may be connectec with, what their genes do and how the mutations affect that gene's function? That's something I would want to know from such a study.

In fact I HAVE to know this in order to know how to think about mutations at all. Evolutionists ASSUME this is how all alleles are made, but I can't assume that and I doubt it seriously and I see no evidence in such a study for this assumption. To my mind these mistakes could very well just BE mistakes, perhaps not deleterious in all cases, perhaps occasionally mildly useful, but mistakes nevertheless, nothing that could produce alleles that code for normal traits in organisms -- traits of the sort studied by Mendel for instance at least, blue eyes, coat color -- anything in the usual phenotypic range that we can observe. Could just simply not the normal way the system is supposed to work. A pathology. It's not that I can't accept it if you can show it, I just do not see it here.

Faith writes:
Well, if you assume evolution, nothing [is to stop beneficial mutations from happening], but if like me you don't, you'd have to prove that they happen at all -- any that actually form useful alleles, that is. Honestly, I haven't seen it yet. Discussions of mutations still sound awfully hypothetical, EXCEPT for the ones they know about that cause diseases -- and there are thousands of those.

Well I see I'm getting repetitive as I elaborated the same point above.

There have been hundreds of scientific studies that have conclusively demonstrated that mutations happen. There is no way to realistically deny that mutations happen.

Um, I have to ask here what SORT of evidence is involved in these studies generally? Since sequencing the genome is a very rare study, you have to be talking about traits that appear in the phenotype, no? Or perhaps changes at individual genes whose function it has been possible to identify? Again, my doubt is that the known mutations have been shown to be anything along the lines of what I'm calling "normal" alleles. This seems to be assumed but never demonstrated. No?

Given that, we then have to decide what constitutes a ďbeneficialĒ mutation, and why this would represent a special case of a mutation that cannot happen.

Well, the creationist thought that comes to mind is that there's no reason to expect that it WOULD happen IF mutations are NOT the normal source of (normal) alleles after all, as of course creationists suspect. The idea that ANY mutation could be beneficial (in the sense of a normal allele as I'm talking about it though I may need a better word) is a logical assumption that follows upon the assumption that the theory of evolution is true.

But it MUST be demonstrated to a creationist, because we simply can't assume it. If you can really demonstrate it, we'd have to accept it. But this whole discussion so far is the usual hypothetical discussion. You see changes in the genes, yes, they are mutations by definition, yes, but what they DO is the crucial thing and that part is assumed except for the ones you can document that do ABNORMAL things to the phenotype, or that don't appear to do anything. You are arguing that there's no reason for them not to be beneficial only BECAUSE if evolution is true there is no reason for them not to be. For this reason you've GOT to show something real in the genome. You can't expect us to accept your field correlates or however you put that.

When we add to this the simple observation that the occurrence of mutations is not sensitive to the phenotypic effects that the mutation would have on the organism, I donít see how there is anything that could stop a beneficial mutation from happening.

I don't know what you mean by "not sensitive to the phenotypic effects that the mutation would have on the organism." I've been struggling to get it, finally gave up.

In terms of the scientific method, the default conclusion is that beneficial mutations can and do happen.

For reasons said above, can't accept "default conclusion," need an actual allele for an actual phenotypic effect that's an interesting variation and not a deformity. If such exist, shouldn't you be able to come up with at least ONE?

The alternative is to propose that there is a special mechanism in place that prevents mutations from happening if those mutations would have a positive effect on phenotype.

Not if, as creationists believe, alleles are part of the original creation, built in from the beginning and not evolved. What we actually see of mutations so far, the actual evidence, is of changes that either do bad things or nothing much at all or at best make a mild sort of change that's hard to pin down (and I'm not even sure that this has been demonstrated really).

If the assumption is correct that beneficial mutations MUST happen you MUST be able to demonstrate one. There's really no reason why you can't if the assumption is true. Or, let me ask, what IS the reason you have for this inability to demonstrate it?

A mere assumption based on evolutionary theory doesn't do it for us.

Since there is no evidence for such a special mechanism, there is no reason to think that beneficial mutations are different from any other kind of mutation in terms of whether or not they can happen.

Again, there's no need for a special mechanism if what mutations really are is simply mistakes in the coding system, that is, a pathology of the reproductive system, that aren't desirable for the organism -- in a general sense at least if not always an obvious specific sense -- which is what the evidence so far seems to show. The odd thing in that case would BE the production of a beneficial mutation, and it COULD happen since it's all just chemicals strung together, but it would be the improbable event.

It can be extremely difficult to identify ďbeneficialĒ mutations, because ďbenefitĒ is highly context-specific. For instance, mutations have been identified that cause plants to grow taller than they otherwise would. This would be beneficial where competing plants were tall, because it would allow the plant to reach sunlight, but it would not really be useful for a plant that has little competition for sunlight.

Yes I get the context-specific thing, but any organism has a collection of alleles that appear to be context-specific, don't they? Normal occurring or "old" alleles. This is the stuff that selection works on. Clue me in on this example. How exactly do you know this is a "mutation" and not just a rare, perhaps recessive, allele that happened to show up? Has the gene actually been studied so its sequence is known (just the gene, not the whole genome)?

However, many kinds of detrimental effects can be easily identified because of the obvious deformities they cause. This is the only really sure reason why we know so many more detrimental mutations than beneficial mutations.

Yes. But the fact that this sort of effect IS easily identified, while beneficial effects are as good as nonexistent to the naked eye, appears to support the creationist interpretation more than the evolutionist interpretation.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.


This message is a reply to:
 Message 28 by Blue Jay, posted 04-06-2010 7:21 PM Blue Jay has responded

Replies to this message:
 Message 30 by Blue Jay, posted 04-07-2010 10:43 AM Faith has responded

    
Blue Jay
Member (Idle past 165 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


(1)
Message 30 of 87 (554311)
04-07-2010 10:43 AM
Reply to: Message 29 by Faith
04-06-2010 10:07 PM


Re: evidence for mutations.
Hi, Faith.

First off, you are overusing the word ďassumptionĒ: an assumption is something that cannot be based on anything. Since the idea of beneficial mutations is based on the observation that mutations occur, it is not an assumption.

A hypothetical scenario is not even remotely similar to an assumption. Please stop flinging the word ďassumptionĒ around.

-----

Faith writes:

For reasons said above, can't accept "default conclusion," need an actual allele for an actual phenotypic effect that's an interesting variation and not a deformity.

Then you are asking for evolutionists to provide a level of proof that you would never ask of anybody else for any other claim!

If I could prove to you that humans can walk, would you then demand additional evidence that shows that humans can walk to a water hole to get water? You would not demand this, because you know that the destination has no relevance whatsoever for the mechanism of getting there. If I can walk, I can walk to water. Period.

But, in the case of mutations, youíve totally flip-flopped your position, and are demanding that, after we have proven the proverbial ability to walk, we still have to prove the proverbial ability to walk to water.

The functionality of the allele has absolutely nothing to do with whether or not the mutation that would create the allele can happen. So, if I can show you that a new allele can be produced (and I have done so), then I have shown you the ability to make a beneficial mutation. No assumptions are involved at all in this conclusion: every step of the process is supported by evidence. If a gene can change, it can change into something functional. Period.

-----

Faith writes:

Again, there's no need for a special mechanism [to prevent beneficial mutations] if what mutations really are is simply mistakes in the coding system, that is, a pathology of the reproductive system, that aren't desirable for the organism -- in a general sense at least if not always an obvious specific sense -- which is what the evidence so far seems to show.

emphasis added

Once again, desirability has nothing to do with the mechanisms of allele production.
What part of that is so hard to understand?

-----

Faith writes:

...from this study it doesn't appear that you know anything about [the mutations] that would validate the assumption that all alleles originated with this kind of event, which IS the assumption of evolution, right?

Okay, now youíre moving the goalposts. Why do I have to demonstrate that all alleles emerged this way? If I demonstrate that one alleles emerged this way (which I have done), I am vindicated, because it then falls on you to show that other alleles are somehow different from that allele.

Besides, youíre reading everything we do in science backwards from the way it actually happens. Scientists started with the observation that mutations produce new alleles, and extrapolated that backwards to hypothesize that all alleles emerged this way. Since no one has produced evidence for any other mechanism by which alleles are generated, mutation is currently the only demonstrated way to explain the origin of alleles.

Until somebody presents something better, this is what we have to work with to explain the genetic diversity of life. So, thatís what we use to construct our current model of life and its history. If you disagree with this model, the onus is on you to demonstrate that reality deviates from the model, not on us to provide better proof of what we have already demonstrated to be accurate.


-Bluejay (a.k.a. Mantis, Thylacosmilus)

Darwin loves you.


This message is a reply to:
 Message 29 by Faith, posted 04-06-2010 10:07 PM Faith has responded

Replies to this message:
 Message 31 by Faith, posted 04-07-2010 4:19 PM Blue Jay has responded

  
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