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Author Topic:   Reduction of Alleles by Natural Selection (Faith and ZenMonkey Only)
Blue Jay
Member (Idle past 1394 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 1 of 87 (553158)
04-01-2010 4:59 PM


GREAT DEBATE: FAITH AND BLUEJAY ONLY!

I would like to continue the discussion Faith began in The End of Evolution By Means of Natural Selection in the Great Debate forum, if she is interested in continuing it.

I’ll focus my comments on this portion of her OP there:

Faith writes:

But whether we are talking only about a change in a single trait or in many traits at once, the trend is ALWAYS toward genetic depletion. You can add as many new alleles as you think mutation can come up with at any point in this progression, but when these selection and isolating processes go to work on them the very same thing happens. You may get a new trait but you'll always get it at the expense of all the other genetic possibilities, and when this occurs with many traits you eventually get speciation, fixed loci, and such limited ability for further variation evolution is for all intents and purposes at an end.

This topic has caused a lot of frustration (primarily for Faith herself), so I’ll try to tread softly and take it easy. I’ll provide a basic comment on each sentence from the above quotation: these will serve as prompts that can be used by Faith to start her side of the discussion however she chooses.

Faith, please let me know what I may have misunderstood from your statements, and help me find if and where I'm off base on any or your points.

Faith writes:

But whether we are talking only about a change in a single trait or in many traits at once, the trend is ALWAYS toward genetic depletion.

I can only address this statement by appealing to mutation, which is known to happen at extremely higher rates than natural selection happens. If mutation is disallowed, then this statement may very well be quite true.

However, if mutation is allowed, then it becomes a question of comparing the rate of selection-mediated diversity loss to the rate of mutation-mediated diversity gain.

Do you agree with that?

-----

Faith writes:

You can add as many new alleles as you think mutation can come up with at any point in this progression, but when these selection and isolating processes go to work on them the very same thing happens.

For this one, we need to consider a timeline of events, including the following events:

  1. Onset of selection pressure
  2. Emergence of new alleles
  3. Extermination of alleles selected against

And, the following considerations:

  1. Other concurrent selection pressures
  2. Genetic linkage between different alleles
  3. Magnitude of each selection pressure

If we choose to pursue this complex model, I think we’ll quickly find that decreasing genetic diversity is not so inevitable as you have argued. I'll hold off on the specifics until you're ready to discuss it.

-----

Faith writes:

You may get a new trait but you'll always get it at the expense of all the other genetic possibilities, and when this occurs with many traits you eventually get speciation, fixed loci, and such limited ability for further variation evolution is for all intents and purposes at an end.

I explained a bit about genetic fixation in a few other places. Fixation is what you’re talking about: the elimination of all alleles for a certain gene except for one.

I do not think that fixation is inevitable, and I’m certain will never occur at all positions in the genomes of all individuals within a single population.

Selection pressures simply cannot be orchestrated such that any single organism can contain all the “best” alleles for all genes: so, naturally, we should expect that no single combination of alleles will be absolutely superior to all other possibilities in a population.

As an example, let me present Uta stansburiana, the “rock-paper-scissors” lizard I referred to earlier in your thread. This is an (admittedly unusual) example of a population that has reached a relatively stable balance between different genotypes. This sort of “balancing act” is what is going on in nearly all populations, all the time: the equilibrium oscillates between different character states, occasionally leading to the complete extinction of a certain trait, but also often leading to a complete rebound of a rare allele.

-----

I look forward to your responses, and I hope I won’t upset you and frustrate you too much in our discussion.

Edited by Bluejay, : Some reformatting, "do you agree with that?" and "I'll hold off on the specifics until..."

Edited by Bluejay, : Alter title in accordance with Faith's wishes.

Edited by Bluejay, : No reason given.

Edited by Admin, : Change title now that ZenMonkey is taking over for Bluejay.


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

Darwin loves you.


Replies to this message:
 Message 3 by Faith, posted 04-02-2010 7:58 AM Blue Jay has responded
 Message 5 by Faith, posted 04-03-2010 6:07 PM Blue Jay has responded
 Message 15 by Faith, posted 04-04-2010 1:07 AM Blue Jay has not yet responded
 Message 16 by Faith, posted 04-04-2010 2:40 AM Blue Jay has responded

  
Blue Jay
Member (Idle past 1394 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 4 of 87 (553281)
04-02-2010 1:36 PM
Reply to: Message 3 by Faith
04-02-2010 7:58 AM


Hi, Faith.

I've altered the title in accordance with your preferences. I agree: let’s take our time on this, and make sure we’re communicating effectively.

In that spirit, I wanted to ask for a bit of elaboration/clarification:

Faith writes:

I don't believe that TRAITS are reduced; in fact they're increased in the scenario I have in mind. The way I picture it, it's ALLELES that are decreased AS new traits emerge.

How do you envision new traits emerging? Not by mutation, I gather?

Having traits and alleles show different diversity patterns seems contradictory to me. Granted, there isn’t a one-to-one correlation between allelic diversity (you can have some traits that emerge without new alleles emerging, and you can have new alleles emerge without producing any new traits), but I would think that there should be a general trend of correlation between allelic and trait diversity, given that all traits ultimately trace back to alleles.

I’m also uncertain as to how trait diversity is increasing in your scenario.

I would appreciate any explanation or clarification on this point. Take whatever time you need or want to do so.

-----

In the meantime, perhaps a bit of terminology would be beneficial, just to make sure we’re both clear on what we’re talking about:

gene: a region of the genome that encodes a certain product
allele: one of several sequence variants of a gene

character: a physical attribute of an organism
trait: one of several variants of a character

genotype: a suite of alleles in a single organism
phenotype: a suite of traits in a single organism

Also, are you familiar with the mechanisms of mutation and evolutionary genetics (e.g., crossing over, independent assortment, point mutations, insertions/deletions, etc.)? We might not need to talk about these, but, just in case...

-----

I look forward to this: it’s going to be fun. Except, now it seems that we're going to have an audience with commentary privileges. I hope I don't get camera-shy.


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

Darwin loves you.


This message is a reply to:
 Message 3 by Faith, posted 04-02-2010 7:58 AM Faith has responded

Replies to this message:
 Message 8 by Faith, posted 04-03-2010 11:08 PM Blue Jay has responded

  
Blue Jay
Member (Idle past 1394 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 6 of 87 (553526)
04-03-2010 7:26 PM
Reply to: Message 5 by Faith
04-03-2010 6:07 PM


Re: graphic attempts
Hi, Faith.

Faith writes:

Bluejay writes:

However, if mutation is allowed, then it becomes a question of comparing the rate of selection-mediated diversity loss to the rate of mutation-mediated diversity gain.

Do you agree with that?

No I don't. This is what everybody keeps saying and while I have the picture in my mind of how you're all wrong I haven't been able to get it said in a satisfactory way.

I think you’re expressing yourself just fine: it’s perfectly coherent and it’s a great basic explanation of the process of natural selection.

My only point of confusion is why you think this process will inevitably lead to complete allele depletion. I think that’s going to be too big a question to try to tackle in one step, so let me ask a simpler question (and a follow up):

Do you agree that, if mutation is allowed, then new mutations can, at least in principle, produce new alleles?

If so, doesn’t basic reasoning tell us that the change in diversity can be determined by comparing the number of new alleles produced by mutations to the number of old alleles exterminated by natural selection?

-----

Keep in mind, we’re still just considering one gene here. I don’t want to get into a multiple-gene scenario until we’ve cleared up how to measure changes in diversity for one gene.


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

Darwin loves you.


This message is a reply to:
 Message 5 by Faith, posted 04-03-2010 6:07 PM Faith has responded

Replies to this message:
 Message 7 by Faith, posted 04-03-2010 8:51 PM Blue Jay has responded

  
Blue Jay
Member (Idle past 1394 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 9 of 87 (553564)
04-03-2010 11:18 PM
Reply to: Message 7 by Faith
04-03-2010 8:51 PM


Re: graphic attempts
Hi, Faith.

Let me clear up a couple managerial type things here. I’ll post a response to the “meaty” portions of your post in a second reply to follow shortly after this one.

Faith writes:

But it does seem that if I were getting it across you would have had a title that reflected it.

I humored you on the title.

selection doesn’t work on alleles, it works on traits. If an organism has camouflaged coloration, natural selection doesn’t care if its genotype is Aa or AA. So, the only thing natural selection can actually reduce directly is traits. Because alleles are the cause of these traits, natural selection working on these traits will necessarily impact the alleles, too.

There really wasn’t anything wrong with the title I proposed: it said exactly what I wanted it to say. I changed it because I wanted to avoid this little discussion until the Great Debate had been agreed upon and established.

On a somewhat related note, I also apologize for not having posted a message at your topic informing you of this debate (that’s standard etiquette). I wanted to wait until was promoted, but, by then, Percy had already posted the note.

-----

Faith writes:

Bluejay writes:

My only point of confusion is why you think this process will inevitably lead to complete allele depletion.

It doesn't necessarily even if you get speciation, I've tried to stick to saying genetic REDUCTION.

A thread with two wordsmiths can be extremely trying on everybody’s patience. This is me talking from personal experience.

I had originally written “extinction,” and then thought better of it and switched it to “depletion,” which is a slightly softer word that still conveys a similar idea. Unfortunately, I forgot to edit out “complete.” I guess “reduction” could be seen as slightly softer than “depletion,” but I don’t see a meaningful distinction to be made there, and my usage of “depletion” wasn’t intended as anything different from your usage of “reduction.”

Let’s just agree not to get too picky about semantics outside of the usage of well-established terminology (trait, allele, gene, etc.): I think we’ll both be happier that way.

-----

Faith writes:

Bluejay writes:

Keep in mind, we’re still just considering one gene here. I don’t want to get into a multiple-gene scenario until we’ve cleared up how to measure changes in diversity for one gene.

OK, well I got ahead of you then.

Well, no you didn’t: I was only referring to my own post. I’ll remember never to use the royal “we” outside of my kingdom again.


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

Darwin loves you.


This message is a reply to:
 Message 7 by Faith, posted 04-03-2010 8:51 PM Faith has responded

Replies to this message:
 Message 10 by Faith, posted 04-03-2010 11:23 PM Blue Jay has responded

  
Blue Jay
Member (Idle past 1394 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 11 of 87 (553566)
04-03-2010 11:27 PM


Hi, Faith.

You may be going too fast for me now!

My next response may be somewhat less soon than I anticipated. I should be able to get it out tonight sometime.

Thanks.


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

Darwin loves you.


Replies to this message:
 Message 12 by Faith, posted 04-03-2010 11:33 PM Blue Jay has not yet responded

  
Blue Jay
Member (Idle past 1394 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 13 of 87 (553571)
04-03-2010 11:57 PM
Reply to: Message 8 by Faith
04-03-2010 11:08 PM


The crux
Hi, Faith.

I was going to make a detailed, step-by-step response to all of your points, but I think it would be more effective to focus on just the elephant in the room, now that I am aware that it's there.

Faith writes:

[New traits emerge by] the coming to the fore of previously unexpressed alleles, probably mostly recessive ones in some cases (these technical things I'd like to know more about), by new combinations of alleles getting an opportunity to be expressed and that sort of thing.

This contradicts the main point of your argument, and is really the crux of the argument I’ve been trying to bring against you.

You have been arguing that natural selection should eliminate most of the genetic diversity in a population. You have a parent population with all kinds of allelic diversity in a model where allelic diversity is inexorably reducing over time. So, why shouldn’t this process also be working in the parent population? What is different about the parent population that allows it to maintain high levels of genetic diversity?

Edited by Bluejay, : No reason given.


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

Darwin loves you.


This message is a reply to:
 Message 8 by Faith, posted 04-03-2010 11:08 PM Faith has responded

Replies to this message:
 Message 14 by Faith, posted 04-04-2010 12:29 AM Blue Jay has responded

  
Blue Jay
Member (Idle past 1394 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 1394 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 won’t 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 you’re just arbitrarily choosing what variables can and can’t 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.


This message is a reply to:
 Message 14 by Faith, posted 04-04-2010 12:29 AM Faith has not yet responded

Replies to this message:
 Message 20 by Admin, posted 04-04-2010 1:22 PM Blue Jay has not yet responded

  
Blue Jay
Member (Idle past 1394 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

  
Blue Jay
Member (Idle past 1394 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 1394 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 1950’s 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, let’s consider the Northern elephant seal. According to the Wiki article, they reached their low point (total population less than 1000 individuals) in the late 1800’s/early 1900’s. 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. Let’s try to apply the human mutation rate to the elephant seals and see what their genetic diversity is like today (don’t worry: I’m not particularly mathematically inclined, either---as you can see by my math needing to be clarified by Admin).

So, let’s 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 population’s 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

  
Blue Jay
Member (Idle past 1394 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 don’t we slow down? I’m 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 weren’t even aware of what function DNA performed. All we can really do is learn to do it right in the next study.

If you’d 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, I’ve 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 it’s got precedent, and the tools are becoming more accessible, I’m 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 shouldn’t 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 weren’t getting anywhere with you repeating the same thing over and over again; and, since I’m 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

  
Blue Jay
Member (Idle past 1394 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 don’t 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 I’ll be dead by then, too.

-----

Faith writes:

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

Well, I didn’t: 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 children’s sequence differed from both parents’ genomes. Each child’s genome contained about 70* places that differed from both parents’ genomes.

That’s 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 “beneficial” 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 don’t 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 “beneficial” mutations, because “benefit” 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

  
Blue Jay
Member (Idle past 1394 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 “assumption”: 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 “assumption” 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, you’ve 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 you’re 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, you’re 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, that’s 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

  
Blue Jay
Member (Idle past 1394 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


(1)
Message 32 of 87 (554382)
04-07-2010 11:05 PM
Reply to: Message 31 by Faith
04-07-2010 4:19 PM


Re: evidence for mutations.
Hi, Faith.

I’m as frustrated as you are: my points are also being ignored, misunderstood and misrepresented. But, from my perspective, it does not feel like you’re making a good-faith effort to understand what I’m saying to you. I have addressed your points, but my addressing them seemingly has no effect on how your next post is going to be composed.

At any rate, your last post seemed like a lot of quasi-controlled ranting. You started talking about things that don’t make any sense at all (for instance, what is a “normal allele”?), and you seemed to have started thinking that alleles that cause deformities or other debilitations are not “alleles,” which is false and may have been a source of confusion about my arguments.

I’m not going to respond directly to any comments you made, because I don’t think I have the maturity to handle that appropriately. Instead, I’m going to try to summarize the main thrust of my argument.

I have been trying to get you to see that you are looking at this situation in an entirely inappropriate light. I have uncovered the two major points of contention that you have with the evolutionist argument, and I will now provide what I think are accurate rebuttals to those two points:

  1. The difference between beneficial and deleterious mutations.

    There is no difference between beneficial and deleterious mutations. At least, not for the molecules that cause them. At the molecular scale, a mutation is only a switch from an A to a T, or something akin to that. To the molecules, there is no “beneficial” or “deleterious”: they do not directly experience either one.

    So, the monikers “beneficial” and “deleterious” do not apply to the mechanism of mutation. They only apply to the phenotype of the resulting allele. So, arguments about the mechanism of the mutation apply equally as well to mutations that would have a beneficial effect and to mutations that would have a deleterious effect. There is no mechanistic distinction between beneficial and deleterious mutations, so classifying them as "beneficial" and "deleterious" when discussing if and how they happen is meaningless: rather, we should be categorizing them mechanistically: i.e., "point mutations," "insertions," "deletions," etc.

    This was where the walking analogy came in. Walking is walking. There is no mechanistic difference between walking to the store and walking to the park: in both cases, the same mechanism is used to get there.

    Likewise for mutations. Mutations are mutations. There is no mechanistic difference between mutating into a beneficial allele and mutating into a deleterious allele: in both cases, the same mechanism is used to get there.

    A beneficial mutation is just a specific case of a mutation, just as walking to the watering hole is just a specific case of walking. There's no reason to think it is somehow different from every other case of mutation/walking. That was the point of the analogy.

    Do you understand what I’m saying?

    For the record, I also feel like I am being made to cross all the t’s and dot all the i’s for you: you come off as an idiot to me as much as I come off as an idiot to you. We can solve this by (1) repeatedly libeling each other and calling each other idiots or (2) trying to understand each other in the hope that understanding will cure each other’s idiocy.

  2. What is based on what?

    You think our argument unfolds as follows:

    (1) Assume that all alleles come from mutations.
    (2) Observe an allele that we have never seen before.
    (3) Conclude that the allele came from mutation.

    In actuality, our argument unfolds as follows:

    (1) Demonstrate that mutations create new alleles.
    (2) Observe that no other means of creating alleles has been demonstrated.
    (3) Disregard these undemonstrated means of creating alleles.
    (4) Conclude that, to the best of our knowledge, all alleles come from mutations.

    Then, only after that, we tack on two more steps:

    (5) Observe an allele that we have never seen before.
    (6) Conclude that the allele came from mutation.

    Your argument is that the first three steps never happened. This is simply false.

    I’ll grant that some of us may get overzealous about our conclusion, and may not treat it with the proper air of tentativity, but it really is the only conclusion that can be arrived at by only using processes that have been demonstrated to happen. I don't see how logic could allow any other progression of thought on the subject.

    The only remedy for this is to demonstrate that some other process that produces alleles is happening (e.g. an Intelligent Designer). In the absence of that, we literally have no choice but to fall back on mutation as the only possible explanation.

    There is no sense in demanding that I prove that mutations could have caused situation X when it has already been shown that mutations have caused things that are mechanistically indistinguishable from situation X, and when nobody has been able to demonstrate that a suitable alternative explanation is viable.

-----

I believe I have accurately represented your views here, and have provided solid rebuttals that should clear up your misgivings about the reasons we support mutation as the primary source of genetic diversity.

I don't expect that this will change your mind about whether alleles arise by mutation, but I hope it will at least put an end to your inaccurate portrayals of our arguments and methods of reasoning.

If you take these points under consideration, I think we're prepared to discuss the role of mutation in the processes of speciation and diversification.

Edited by Bluejay, : "-----"


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

Darwin loves you.


This message is a reply to:
 Message 31 by Faith, posted 04-07-2010 4:19 PM Faith has responded

Replies to this message:
 Message 33 by Faith, posted 04-08-2010 12:06 AM Blue Jay has responded
 Message 34 by Faith, posted 04-08-2010 1:25 AM Blue Jay has not yet responded

  
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