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Author Topic:   Mutation
crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 46 of 171 (98560)
04-07-2004 9:19 PM
Reply to: Message 43 by Servus Dei
04-07-2004 8:41 PM


How might one define a mutation?
Any sequence of genetic code that you didn't inherit from either of your parents.
What are some common day examples of beneficial mutations in humans?
People with no wisdom teeth. There's a number of mutations, I believe, that confer degrees of resistance to various diseases, like the gene for sickle-cell anemia.
Aren't most mutations sterile, or unable to reproduce?
Certainly not. You have somewhere between 50 and 500 mutations of your very own, and I assume you have no reason to doubt your fertility?
I thought that mutations more often take things away than provide new, helpful things.
All mutations have the potential to do is change how protiens are created, because that's all genes do - code for protiens.
It seems like when people refer to "beneficial" they mean two things: Helpful to the organism, and able to make reproduction faster and more numerous. Is this equiviating on the term?
Not exactly - it's generally possible, given a substantial enough mutation, to predict how it might interact with the environment. For instance in an environment dominated by nylon oglimers, a mutation allowing a bacterium to digest them is likely to be beneficial indeed. Ultimately, though, you have to go by the results - does that gene spread through the gene pool, or is it eliminated?
For example, when mutations take out teeth, that is not exactly beneficial, is it?
Ask somebody with impacted wisdom teeth if not having them would be beneficial. In an environment of cooked, soft food leading to smaller jaws with less room for teeth, less teeth is beneficial indeed.
The problem is that, as humans, we pre-empt natural selection. We don't allow selection to occur, so ultimately it's not possible to use "beneficial" properly in regards to human mutations. Human allele frequencies change in ways that have nothing to do with natural selection or adaption to environment.
What would you say is the difference between evolution and speciation?
Evolution is the process by which allele frequencies within a gene pool change. Speciation is the process by which gene pools sepearate into separate pools.
If you're not looking at evolution from the perspective of population genetics, you're not looking at it the right way.
If so, what is the organism evolving into that is new?
Organisms don't evolve. Only populations do.
Finally, are evolutions and mutations somewhat synomous, or is there no direct relation?
Mutations are novel gene sequences not inherited from either parent. Evolution is a change in allele frequencies. The source of new alleles is mutation, but mutation isn't responsible for the shift in frequency - that's a function of natural selection. It is safe to say that mutation + natural selection = evolution.

This message is a reply to:
 Message 43 by Servus Dei, posted 04-07-2004 8:41 PM Servus Dei has replied

Replies to this message:
 Message 50 by Wounded King, posted 04-08-2004 6:43 AM crashfrog has replied
 Message 54 by Servus Dei, posted 04-09-2004 3:13 PM crashfrog has replied

  
Milagros
Inactive Member


Message 47 of 171 (98577)
04-07-2004 11:28 PM
Reply to: Message 43 by Servus Dei
04-07-2004 8:41 PM


Re: More Questions...
Servus Dei
"What would you say is the difference between evolution and speciation? Can evolution occur without speciation? If so, what is the organism evolving into that is new? Can there be any significant evolution within a species? Finally, are evolutions and mutations somewhat synomous, or is there no direct relation?"
Servus, just to be clear, I don't want to assume anything whether you understand this or not, but when you say "evolution" there is a distinction that is made between the "type" of evolution you are talking about.
"In evolutionary biology today, macroevolution is used to refer to any evolutionary change at or above the level of species. It means the splitting of a species into two (speciation, or cladogenesis, from the Greek meaning "the origin of a branch") or the change of a species over time into another (anagenesis, not nowadays generally used). Any changes that occur at higher levels, such as the evolution of new families, phyla or genera, is also therefore macroevolution, but the term is not restricted to the origin of those higher taxa.
Microevolution refers to any evolutionary change below the level of species, and refers to changes in the frequency within a population or a species of its alleles (alternative genes) and their effects on the form, or phenotype, of organisms that make up that population or species.
Another way to state the difference is that macroevolution is between-species evolution of genes and microevolution is within-species evolution of genes."
You will find this on: Macroevolution: Its definition, Philosophy and History
So you see when you ask, "What would you say is the difference between evolution and speciation? Can evolution occur without speciation?" To your first question that would depend if you are referring to Macro or Micro-evolution. If you are referring to Macro, then as the paragraph above explains there really is no difference. If you mean Micro then yes there is. For your second question, again, if you mean Micro-evolution then yes micro can occur without speciation in contrast to Macro which couldn't.
[This message has been edited by Milagros, 04-07-2004]

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NosyNed
Member
Posts: 8996
From: Canada
Joined: 04-04-2003


Message 48 of 171 (98603)
04-08-2004 1:36 AM
Reply to: Message 38 by Milagros
04-07-2004 2:52 PM


Not good logic
But notice he does say that MOST ARE "harmful" or "neutral". I'm not talking about any "beneficial" ones, I am ONLY addressing your response where you claim that "This is false...." to the statement made earlier that "Most mutations are harmful".
But the statment:
"Most mutations are harmful or neutral" can be true
AND at the same time
"Most mutations are harmful" can be false.
If 1% of mutations are beneficial, 25% are harmful and 74% are neutral then that is the case.
I don't even know if we actually no what the real proportions are. It may well be that we see "most" mutations (well over half) as being neutral because we don't count all the non-viable fetuses that never make it beyond very early stages of gestation.
Let's say in everything that lives to birth it is probably true that the majority of mutations are neutral since all of us, for example, have several.

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RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 49 of 171 (98606)
04-08-2004 2:03 AM
Reply to: Message 48 by NosyNed
04-08-2004 1:36 AM


Re: Not good logic
because we don't count all the non-viable fetuses that never make it
why stop there? what about all the eggs that were not fertilized due to mutations possible to {sperm \ egg} so incompatable?

we are limited in our ability to understand
by our ability to understand
RebelAAmerican.Zen[Deist
{{{Buddha walks off laughing with joy}}}

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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 50 of 171 (98642)
04-08-2004 6:43 AM
Reply to: Message 46 by crashfrog
04-07-2004 9:19 PM


Tut! Tut!
Crash writes:
All mutations have the potential to do is change how protiens are created, because that's all genes do - code for protiens.
Dearie me Crash,
That is a really lamentable oversimplification of things. Even allowing for the argument that a gene is simply DNA coding for a protein there is still huge potential for mutation in the many non protein coding regulatory elements that determine where and how much of a specific protein is expressed as well as novel functions for non protein coding mRNAs such as the repressor functions of microRNAs.
TTFN,
WK
[This message has been edited by Wounded King, 04-08-2004]

This message is a reply to:
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Replies to this message:
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crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 51 of 171 (98645)
04-08-2004 8:34 AM
Reply to: Message 50 by Wounded King
04-08-2004 6:43 AM


That is a really lamentable oversimplification of things.
Perhaps you're right. Nonetheless I think it's useful to take a step back and consider what is really meant when we say "this gene codes for such-and-such." Otherwise one is liable to conflate the complexity of a structure with the complexity of the gene controlling it, which leads to dumb questions about how much complexity mutation can be the source of, etc.

This message is a reply to:
 Message 50 by Wounded King, posted 04-08-2004 6:43 AM Wounded King has replied

Replies to this message:
 Message 52 by Wounded King, posted 04-08-2004 9:39 AM crashfrog has replied

  
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 52 of 171 (98651)
04-08-2004 9:39 AM
Reply to: Message 51 by crashfrog
04-08-2004 8:34 AM


I'm not sure that that is neccessarily a dumb question. It is a very complicated one in many ways.
If you look at the complexity of many gene networks for producing a particular structure, say the development of the wing for arguments sake, the different individual mutations could lead to a great array of levels of deviation from Wild Type development. With a range going from total loss of a protein and thereby a whole signalling pathway to small amino acid changes leading to slightly enhanced/ decreased binding affinities.
The more connections a gene has in a particular network and the more fundamental the position of that gene/ network in subsequent developmental stages the greater the complexity of the events downstream will be, unless of course it just kills the thing stone dead and nothing ever happens again, i.e. something that interrupts initial antero-posterior patterning has farther reaching consequences than something which disrupts the identity of your individual digits.
In fact there are some papers suggesting that the more binding partners a protein has the more likely it is to have a conserved structure and other suggesting that this is not the case and highly connected proteins are just as prone to mutation. So whether the complexity of a proteins interactions affects its conservation is an ongoing topic for discussion.
I think that the complexity of consequences arising from a specific mutation is a reasonable thing to think about, as long as people realise that the answer is going to be different for almost every gene.
[This message has been edited by Wounded King, 04-08-2004]

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crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 53 of 171 (98657)
04-08-2004 10:12 AM
Reply to: Message 52 by Wounded King
04-08-2004 9:39 AM


I think that the complexity of consequences arising from a specific mutation is a reasonable thing to think about, as long as people realise that the answer is going to be different for almost every gene.
With that caveat, I agree.

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Servus Dei
Inactive Member


Message 54 of 171 (98940)
04-09-2004 3:13 PM
Reply to: Message 46 by crashfrog
04-07-2004 9:19 PM


Crashfrog,
The people with no wisdom teeth example you sited is not necessarily beneficial. In some people (and I am not sure of the numbers on this), wisdom teeth never affect them in a negative way. I would argue that a lack of wisdom teeth could be beneficial, but is more often neutral, because those people might not have even had a problem with wisdom teeth in the first place. I believe I have heard it said that only about 1/5 of people actually have problems with their wisdom teeth - again, please let me know if I am unreasonably off.
With my question about mutations being sterile, I simply meant I didn't think that those mutations were passed on to various generations in a beneficial way, if at all. I wasn't referring to fertility.
The way one determines how a mutation is beneficial seems somewhat abitrary, since it relies on the environment. Removing that variable, is it impossible to determine if a mutation is beneficial or not? For example, getting a thick mat of hair all over your body would be beneficial in Alaska, but not in a desert. If environment did not matter, the coat wouldn't either, would it?
And thanks for clarifying what evolves, the population, not the organism. Would this mean that I could not evolve, but my son could? In order to evolve, he would need to aquire beneficial traits that I lack, yes?
Up until this point, people have been talking as if there is only one kind of mutation. Would someone be able to give statistics and/or definitions to various kinds of mutations? For example, chromosonal mutations are different than frameshift mutations.
The biology textbook by Miller and Levine (published in 1995, i think), goes into greater detail on this. The text says that a frameshift mutation, in which a single base is inserted or deleted can be lethal. Groups of mRNA are shifted. The result of this mutation is that it could alter the poly-peptide product of a gene. Then the cell would produce the wrong sorts of products, or starve and harm the body.
Chromosomal mutations, such as polyploidy (the condition in which an organism has extra sets of chromosomes) are "almost always fatal in animals."
Now i got this information from their textbook. While I do not completely understand how what they are describing works, it seems clear that mutations are somewhat harmful. It made me wonder about mutations when I didn't find any examples of beneficial mutations in the text. I suppose I might have missed them. If anyone can show me how these mutations work, and how they might be beneficial in the process of evolution (micro or macro), then I would be very appreciative. In the same section (p. 212 and 213), they had examples of mutations that looked nasty, such as a frog with extra hind legs, and that didn't look like it could help the frog in any way.
Finally, I have been hearing things about fruitflies. Many generations of them have been experimented on and introduced to radiation. There were some flies that got 2 sets of wings, but these couldn't even fly. It made me wonder: if we as a guiding intelligence can't even produce a new species of flies by mutations in a lab, how in the world does an unguided nature do it by mutations??? Maybe I haven't been introduced to enough high level reasoning, but it seems at this point in time that relying on mutations to cause any type of beneficial evolution on the large scale and short timeframe that we evolved in is impossible to accomplish by mutations. Are there any examples of major mutations leading to new classes and phyla (when it would be necessary to even create new Kingdoms for the evolutionary theory held today to have credibility? To me, it seems like evolution by mutations is self defeating. Please answer this so that I can understand either where my knowledge is lacking, or (if possible) the theory of evolution is lacking.
Thanks,
Servus Dei

This message is a reply to:
 Message 46 by crashfrog, posted 04-07-2004 9:19 PM crashfrog has replied

Replies to this message:
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JonF
Member (Idle past 168 days)
Posts: 6174
Joined: 06-23-2003


Message 55 of 171 (98954)
04-09-2004 4:23 PM
Reply to: Message 54 by Servus Dei
04-09-2004 3:13 PM


The way one determines how a mutation is beneficial seems somewhat abitrary, since it relies on the environment. Removing that variable, is it impossible to determine if a mutation is beneficial or not?
A mutation that kills immediately is detrimental, no matter what the environment. A mutation in an unused section of DNA that does not activate that section is neutral, no matter what the environment. However, those are special cases; in the general case, you cannot tell if a mutation is beneficial or neutral or detrimental without considering the environment.
If we as a guiding intelligence can't even produce a new species of flies by mutations in a lab, how in the world does an unguided nature do it by mutations???
By literally milions of random trials, filtered by natural selection.
BTW, we have produced new species of flies in the lab. See section 5.3 of Observed Instances of Speciation.

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crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 56 of 171 (98983)
04-09-2004 8:49 PM
Reply to: Message 54 by Servus Dei
04-09-2004 3:13 PM


The people with no wisdom teeth example you sited is not necessarily beneficial
Again, it depends on environment. For people whose jaws are too small to support that many teeth, not having them is beneficial.
But rememeber that humans are no longer subject to the stricter forms of natural selection. The only selection occuring on most humans is sexual selection, really.
I believe I have heard it said that only about 1/5 of people actually have problems with their wisdom teeth
I don't have the stats, myself. I know that mine were removed, so clearly it would have been to my benefit to not have themat all.
With my question about mutations being sterile, I simply meant I didn't think that those mutations were passed on to various generations in a beneficial way, if at all.
You're going to have to explain this. What would prevent a mutation from being passed on? The only mutations we're concerned about are the ones that happen to the fertilized zygote (or during the formation of the gametes in the parents gonands). Since the entire organism is composed of the decendants of that cell, every cell in the organism, including the gametes (well, the ones with the chromosome in question, which would be half of them) will contain the mutant gene.
Where's the problem to heredity, here? I guess I don't understand your point.
The way one determines how a mutation is beneficial seems somewhat abitrary, since it relies on the environment. Removing that variable, is it impossible to determine if a mutation is beneficial or not?
You can never take away environment. You can only change environment. An animal in a scientific pen is still in an environment.
What would be arbitrary would be subjective judgements about what is beneficial or detrimental. Considering mutations in relationship to the environment is the only objective measure of the eventual success of a mutation.
Would this mean that I could not evolve, but my son could?
No... but mutations in your son could represent the evolution of the human population. Your son will always be himself. He'll only change insomuch as humans change throughout their lives. That change will never represent an evolution of your son. It's the difference between your son and you that represent the evolution of the human species.
Then the cell would produce the wrong sorts of products, or starve and harm the body.
Or, confer resistance to disease or give the cell the capability to use a new substance as a metabolic fuel. Or do nothing at all.
While I do not completely understand how what they are describing works, it seems clear that mutations are somewhat harmful.
Again, you seem to be generalizing - because many mutations are harmful or even fatal, you seem to think they all must be.
It made me wonder: if we as a guiding intelligence can't even produce a new species of flies by mutations in a lab
New species of fruitfly? We do that all the time, through reproducive isolation:
quote:
5.3 The Fruit Fly Literature
5.3.1 Drosophila paulistorum
Dobzhansky and Pavlovsky (1971) reported a speciation event that occurred in a laboratory culture of Drosophila paulistorum sometime between 1958 and 1963. The culture was descended from a single inseminated female that was captured in the Llanos of Colombia. In 1958 this strain produced fertile hybrids when crossed with conspecifics of different strains from Orinocan. From 1963 onward crosses with Orinocan strains produced only sterile males. Initially no assortative mating or behavioral isolation was seen between the Llanos strain and the Orinocan strains. Later on Dobzhansky produced assortative mating (Dobzhansky 1972).
5.3.2 Disruptive Selection on Drosophila melanogaster
Thoday and Gibson (1962) established a population of Drosophila melanogaster from four gravid females. They applied selection on this population for flies with the highest and lowest numbers of sternoplural chaetae (hairs). In each generation, eight flies with high numbers of chaetae were allowed to interbreed and eight flies with low numbers of chaetae were allowed to interbreed. Periodically they performed mate choice experiments on the two lines. They found that they had produced a high degree of positive assortative mating between the two groups. In the decade or so following this, eighteen labs attempted unsuccessfully to reproduce these results. References are given in Thoday and Gibson 1970.
5.3.3 Selection on Courtship Behavior in Drosophila melanogaster
Crossley (1974) was able to produce changes in mating behavior in two mutant strains of D. melanogaster. Four treatments were used. In each treatment, 55 virgin males and 55 virgin females of both ebony body mutant flies and vestigial wing mutant flies (220 flies total) were put into a jar and allowed to mate for 20 hours. The females were collected and each was put into a separate vial. The phenotypes of the offspring were recorded. Wild type offspring were hybrids between the mutants. In two of the four treatments, mating was carried out in the light. In one of these treatments all hybrid offspring were destroyed. This was repeated for 40 generations. Mating was carried out in the dark in the other two treatments. Again, in one of these all hybrids were destroyed. This was repeated for 49 generations. Crossley ran mate choice tests and observed mating behavior. Positive assortative mating was found in the treatment which had mated in the light and had been subject to strong selection against hybridization. The basis of this was changes in the courtship behaviors of both sexes. Similar experiments, without observation of mating behavior, were performed by Knight, et al. (1956).
From Observed Instances of Speciation
Remember, it's not the process of mutation alone that gives rise to new species. It's mutations accruing in a situation where gene flow is interrupted (reproductive isolation.)
Are there any examples of major mutations leading to new classes and phyla (when it would be necessary to even create new Kingdoms for the evolutionary theory held today to have credibility?
Here's one, from the same link:
quote:
5.9.1 Coloniality in Chlorella vulgaris
Boraas (1983) reported the induction of multicellularity in a strain of Chlorella pyrenoidosa (since reclassified as C. vulgaris) by predation. He was growing the unicellular green alga in the first stage of a two stage continuous culture system as for food for a flagellate predator, Ochromonas sp., that was growing in the second stage. Due to the failure of a pump, flagellates washed back into the first stage. Within five days a colonial form of the Chlorella appeared. It rapidly came to dominate the culture. The colony size ranged from 4 cells to 32 cells. Eventually it stabilized at 8 cells. This colonial form has persisted in culture for about a decade. The new form has been keyed out using a number of algal taxonomic keys. They key out now as being in the genus Coelosphaerium, which is in a different family from Chlorella.
To me, it seems like evolution by mutations is self defeating.
Only if you assume that all mutations are negative. For some reason we don't seem able to disabuse you of this notion, no matter how many examples of benefical mutations we show you. Why is that?

This message is a reply to:
 Message 54 by Servus Dei, posted 04-09-2004 3:13 PM Servus Dei has replied

Replies to this message:
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 Message 60 by TechnoCore, posted 04-11-2004 6:51 PM crashfrog has replied

  
Servus Dei
Inactive Member


Message 57 of 171 (99262)
04-11-2004 2:27 PM
Reply to: Message 56 by crashfrog
04-09-2004 8:49 PM


Crashfrog,
Thanks for you patience, and for answering all of my questions. I want to continue this, but since it is Easter, I need to wait a couple days until I have the time to properly respond. Just wanted to give you a heads up.
Servus Dei

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NosyNed
Member
Posts: 8996
From: Canada
Joined: 04-04-2003


Message 58 of 171 (99291)
04-11-2004 3:57 PM
Reply to: Message 56 by crashfrog
04-09-2004 8:49 PM


not so fast there
But rememeber that humans are no longer subject to the stricter forms of natural selection. The only selection occuring on most humans is sexual selection, really.
Don't be so sure of this. Just because we don't have lions chasing us doesn't mean that we aren't being selected.
Right now it is possible that addictive physiologies and personalities are being selected against for example. A tendancy to get angry too fast might be selected against (where it may have been selected for in a physically competitive environment. Good parenting instincts for teaching and socializing children may be selected for over the ability to hunt for food.
You are forgetting how very fine the filter is and how subtlely it may act. We don't know what selective pressures we are under.

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Quetzal
Member (Idle past 5872 days)
Posts: 3228
Joined: 01-09-2002


Message 59 of 171 (99310)
04-11-2004 5:58 PM
Reply to: Message 42 by Loudmouth
04-07-2004 4:10 PM


I'm copying the question 'cause otherwise it might be buried.
Loud writes:
Here is a question for the fold. If a mutation causes a change in phenotype, but is neutral with respect to fitness, can this also be considered a neutral mutation? I would assume that this type of mutation would be considered neutral, but was wondering what the uber-experts thought.
I'm not DNAUnion, who's the only self-proclaimed uber-expert on the forum, however I might be able to answer this. Mutations cause (usually minor) changes in phenotype all the time - it's one of the primary means by which variation arises in a population. No sexually-reproducing population is genetically homogenous. Most mutations, regardless of phenotypical effect, are considered neutral because they have no effect on the organism's fitness (which is based on the overall phenotype/environment interaction). IOW, the determination of "neutral" isn't that the mutation has no effect on the phenotype, rather that it is "neutral" in regards to fitness. Anything that increases the organism's marginal fitness is considered beneficial, anything that decreases the organism's marginal fitness is detrimental. Obviously, anything else is neutral.
Where's Mammuthus when we need him? I'm sure he's got 50 or more papers at his fingertips which discuss the issue in great and glorious detail.

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TechnoCore
Inactive Member


Message 60 of 171 (99314)
04-11-2004 6:51 PM
Reply to: Message 56 by crashfrog
04-09-2004 8:49 PM


About the wisdom teeth.
I'd say wisdom teeth really has been an advantage up to modern time.
Most people in primitive societies lost a couple of tooth due to hard life.
Those would have had a better chance of surviving with a couple of replacement-teeth.
But in the year of 2004 having too fit teeth means getting a pair of new ones is a hazard. Strange huh? Selection due to dentist-bills and tooth-paste
[This message has been edited by TechnoCore, 04-11-2004]

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