Is Reproductive Success the Gold Standard?

This is a sincere post. Please don't make the oft' justifiable assumption that you've one of those posters that come in pretending to ask questions when they're really just trying to trip up the pros. I'm a plebe, quite literally. I'm bringing it over here so as not to drag a thread off topic.In a post on another thread I made the following two statements:To this I recieved this response from RAZD:I would be under the impression that I fully understand what was meant if I wasn't finding it impossible to suss any contradiction between this and what I said. I don't know how to elaborate on this to actually form a cogent question. Help!Secondly, to kurseu, Wiki is indeed a wonderful friend; I couldn't post without it. Wiki and Google make up 98.7% of my friends. (Yes, I know I've just implied that the remainder of my friends amounts to only 3.9% of an entity or accumulated parts thereof.)My only understanding was that "specialization" (sorry, totally goofed that) is defined by sexual separation (which makes me and Ronda Kalowinski separate species). As bacteria don't have sex . Now I know, thanks.P.S. for Admin: I know this won't make for a whole topic, but I didn't know where to go. Coffee House?Edited by lyx2no, : Confess my unworthiness.Edited by lyx2no, : Spelling and missed wordsEdited by lyx2no, : No reason given.Edited by lyx2no, : Bad math

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Genesis 2
17 But of the ponderosa pine, thou shalt not eat of it; for in the day that thou shinniest thereof thou shalt sorely learn of thy nakedness.
18 And we all live happily ever after.

Thread moved here from the Proposed New Topics forum.I've promoted it as is but I'd like you and RAZD to figure out a better topic title ASAP. ThanksEdited by AdminNosy, : No reason given.

Try speciation.And I don't think 100-98.7=3.9 (unless you're friends make up more than 100 percent).As to RAZD's comments and yours, I don't see any contradiction either. I think RAZD was just filling out the logical consequence of your points, or clarifying what you meant. Granted, I haven't paid much attention to that thread, so it would be best if he commented.That said, I'm not so sure you should talk about genetic perfection. What is a perfect gene? I'm not aware of such a concept (outside of any discredited eugenics, but their focus was on the perfect race).Also, I think it would be fair to say that there is a template for what a gene should look like. Or better put, what a gene shouldn't look like. Namely, a gene, if it is to be passed on, cannot kill the organism before it can reproduce. Mutations which lower reproductive success (without making it zero) will eventually be pushed out.

While I wouldn't say what you said was wrong, because you mixed in some unscientific concepts it couldn't be considered correct, either. "Genetic perfection"? "Excessive neutral and beneficial genetic variation?" I think this is why RAZD tried to reexpress what you said without the pseudo-scientific mumbo-jumbo.Probably what RAZD objected to most was the phrase "genetic perfection," which means that some genomes must be better than others. But the value of a genome is how well the organism is adapted to its environment. Obviously a species that's going extinct (these days usually because humans have destroyed its native habitat) does not possess a very successful genome for it's environment. And a species that has overpopulated its environment (like human beings) have a very successful genome, but not in all environments. Drop a person into the ocean off Antarctica in winter and see how well he competes with the penguins. Now who has the most perfect genome?So we don't use the term "genetic perfection" - there's no such thing. The proper term is adaptation, and part of what ecologists study is how well or poorly adapted creatures are to their existing environment.There's also no such thing as "excessive neutral or beneficial genes". First, you have a terminology problem, because there's no such thing as a neutral gene. A mutation to a gene can be harmful, neutral or beneficial. In other words, it can be worse, the same, or better than the gene it replaces. Genes themselves are not usually said to be neutral, though you've got the right concept. A gene might be inactive, or turned off, or just have no effect, but I don't think neutral is the correct term for that type of gene.Second, if an organism is well adapted to its environment but 99% of its genes are junk DNA that have no effect, would you call that excessive? Maybe you'd call it inefficient, since each cell division requires copying the 99% useless portion, but now put it in the context of a changing environment, and suddenly that useless DNA serves as a resource for mutation to craft adaptations.And if an organism is poorly adapted to its environment but 99% of its genes are beneficial (and 1% really harmful genes), would you call that excessive?So you can't make judgments on whether genes are excessive are not. The criterion is degree of adaptation to the environment. Other criteria make no sense.--Percy

Thanks for you confidence, lyx2no2, As a point of information, I always treat questions like this as honest inquiries, and will either answer directly or point to another thread where the questions may be more properly discussed (or propose new ones). This is the philosophy of no stupid questions. Of course I have had a number of people try to play games, and when this becomes clear I stop replying to them when there ceases to be a point to accomplish by further posts.There are also people that just seem incapable of understanding the responses, and keep repeating their idée fixe, and these too are best left to themselves. (see MurkyWaters on the definition of evolution, Basic Fundamentals of THE Debate (now open to anyone))I'll go long on this one now: Let us start with a simple distinction: selection occurs at the individual level, evolution occurs at the population level.A phenotype is selected by survival and reproduction, or rejected by death or reproductive failure. A population is made up of a number of individuals, a variety of phenotypes, caused by different mixtures of hereditary traits shared by the population through breeding with some other individual in the population. This is an example of sexual selection occurring at the individual level, rather than speciation. It would only be speciation if it occurred at a population level: one whole population of Lyx2no moresis and one whole population of Ronda Kalowinskius not breeding. Now if all potential mates opt to mate with others rather than a, try as you might, single phenotype, then that would result in reproductive failure of the individual, and the subsequent loss of the particular mix of hereditary traits in that individual (even though the same traits could be preserved in different mixes in other individuals).So yes, for the individual, reproduction is the gold standard for measuring "fitness" of a phenotype within an ecosystem (where there is more to ecology than just environment): presumably you have survived to the point of reproduction, so that element of selection has also been passed.One should not, however, be confused by "most fit" and "genetic perfection" because all you need is adequately fit to survive and reproduce. Adequate is far from perfect, and perfect is likely an elusive goal, particularly when the ecology is constantly changing. The phrase "survival of the fittest" obviously does not apply when there are whole populations of organisms reproducing with varying degrees of success. Yes, I just spent the last 15 minutes reading that article to see how the "problem of speciation" had evolved. Curious that they end up with the same DNA difference as separates humans from chimps. The problem that I have with this "genetic similarity" definition is one of application, I cannot apply such definition to fossil species, just as I cannot apply the "change in frequency of alleles in populations from generation to generation" to fossils. My preference then is to the cladistic model:

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Phylogenetic (Cladistic)/ Evolutionary / Darwinian species

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A group of organisms that shares an ancestor; a lineage that maintains its integrity with respect to other lineages through both time and space. At some point in the progress of such a group, members may diverge from one another: when such a divergence becomes sufficiently clear, the two populations are regarded as separate species. Subspecies as such are not recognized under this approach; either a population is a phylogenetic species or it is not taxonomically distinguishable.

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This works for bacteria, it works for fossils, and it works for sexual species. That's a pretty stiff test.Now if we combine these two definitions into a comprehensive approach, we can use the 98% similarity (whether genetic or morphological cladistically) for "arbitrary speciation," and use known\observed instances of division of a parent population to reproductively isolated daughter populations as "non-arbitrary speciation" (where the important element is not whether they can or cannot interbreed but that they don't). Once interbreeding ceases, gene flow ceases, and the different populations will evolve differently, thus increasing diversity and taking advantage of more ecologies than could be accomplished by adaptation within a single species. Initially they will not be 98% different, so at that point this can be called incipient speciation. Then as evolution proceeds, and an accumulation of differences ultimately reaches 98%, this can then be taken as confirmation that non-arbitrary speciation has occurred by arbitrary speciation standards.In addition arbitrary %change speciation also allows us to monitor change along a lineage that does not have neat divisions of population, and the number of arbitrary speciation events along such a lineage would be a measure of the total accumulated change from ancestor population to descendant population. The "speciation problem" can be characterized by the ring species, where one variety of a species will not interbreed with another, but where interbreeding between other varieties occurs, eventually linking the two varieties genetically through the intermediate (transitional) varieties. If we apply the cladistic plus 98% rule we could (presumably - I don't know the genetic difference between the two) perhaps show that this is not speciation ... yet. This is similar to the other problem with the "biological species" concept when you include "or the potential to mate" into the equation. Certainly you and Ronda have the potential to mate, but we can also mix sperm and egg between S.American Llama and African Camel and produce viable offspring. The inclusion of 98% difference allows us to classify you and Ronda as the same species, but differentiate between Llama and Camel.At the population level we are not concerned whether speciation happens or not, just on what traits allow the continued existence of the population within the ecology. Ecologies change, and populations may evolve adaptations to allow living in different ecologies. These adaptations may result in speciation or they may not, however they should result in adaptation to the new conditions or the population as a whole will be less fit than the previous one was to the previous conditions, and if such ecological change keeps occurring it may drive a species to extinction, which is the reproductive failure of the entire population.So for a population, individual reproduction is important for continuity from one generation to the next, producing enough viable offspring able to reproduce and prevent extinction of the population, but the population does not care particularly which individuals reproduce with which other individuals, nor with which do not reproduce. Looking at evolution of populations, it is more important that hereditary traits be selected that are positive, or neutral, for the continued existence of the population within the ecology du jour. These traits are carried by many individuals within a population in different mixes with other traits, resulting in different phenotypes. While some individuals may perish before passing on certain hereditary traits, others may succeed, some of which may be better than others at survival and reproduction.Enjoy.ps - I will be in Puerto Rico next week on business, and may not have as much opportunity to post.

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we are limited in our ability to understand
by our ability to understand
Rebel American Zen Deist
... to learn ... to think ... to live ... to laugh ...
to share.

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Yeah, I blew it in the original. I wasn't sure it would be cricket to correct it in an implied quote. Your arithmetic is correct but your math is wrong.Wiki is one entity and Google is another. Both together comprising 98.7% of my friends. The remaining 1.3% comprises all other friends put together. This final friend must, therefore, be 3.9% of a single entity or 3.9 % of the accumulated parts of a number of entities. If it, too, were a full entity it would be 33⅓% of my friends, and Wiki plus Google could, at best, be 66⅔% of my friends. If a gene is deleterious to reproduction it's failing to meet the gold standard. What I mean by a lack of template is there is not some immutable gene that can't remain changed even if for the better, because there is something in nature that is going to intentionally change it back to meet some ideal. That would amount to a mechanism preventing micro-evolution from becoming macro-evolution.This isn't to say there is not some type of correction system for DNA. If I remember correctly there is: It can check itself against the other strand. Correct me or fill me in on this too, if you will.

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Genesis 2
17 But of the ponderosa pine, thou shalt not eat of it; for in the day that thou shinniest thereof thou shalt sorely learn of thy nakedness.
18 And we all live happily ever after.

I'm no expert but I'll jump in here. Mostly to beat others so I can be corrected myself.There is a DNA repair mechanism that keeps the rate of mutations in check. I'm not sure you can be correct that it uses the "other strand" because it comes into play when it is replicating a strand. But I don't know.There isn't anything trying to force DNA back to "some ideal". What does exist is selection. Using the oft bandied about statistic that about half of human conceptions fail we see a mechanism weeding about very bad changes.There are some basic genes that are highly conserved. We share them with all (or almost all) life forms. These are those that influence fundamental processes like cell division. It appears that most modifications to them means you get a gene that doesn't work. This may generate some of the failed human conceptions for example. This means that the gene is held in a stable form for a long time. It isn't anything magic it is just the constant removal of anything that doesn't work and it appears that there are few variations on some of these genes that can work.This could be true even if there could be a "better" form of this gene. The gene's environment includes other genes and the chemical processes they end up producing. If a very basic, core gene is changed and it doesn't fit with others then it is removed even if it somehow did it's own specific thing "better". "Better" is always environmentally dependent.

I would fully agree that I should have put "genetic perfection" in quotation marks. Had I considered my own post better I would have done so as I did for "excessive". But at the same time I think "pseudo-scientific mumbo-jumbo" is a bit harsh for a less then formal venue, and better saved for the word-salad boys. I will, nonetheless, take it to heart and let it crush my spirits, Schoolmaster.I meant to imply, and therefore should have said, that all a gene need do to be perfect is get itself preferentially reproduced; that the standard for perfect is simple, not that there is some ideal gene. Rather awkward for a bumper sticker. I had thought, in context, I had expressed that. I was wrong.If the effectiveness of the quotation marks around "excessive" were anything to go by I'm not sure they'd have been a life saver for "perfect".I adopted the "excessive" terminology from those who believe there is a limit as to how far evolution can go based on Biblical notions. If the diminutive quotation marks failed to express my position then clearly my words should have:I'd be a poor champion for that argument as I agree with you.P.S. If I'm one of those word-salad boys, you'll let me know, right?

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Genesis 2
17 But of the ponderosa pine, thou shalt not eat of it; for in the day that thou shinniest thereof thou shalt sorely learn of thy nakedness.
18 And we all live happily ever after.

Hey Ned, Correct, and it usually occurs when the strands are separated for replication. Think of it as a method of quality control, doesn't catch all the mistakes, but does usually find the big ones.In addition this mechanism seems to be (from the result of experiments) subject to variation in reaction to hormones of stress, reducing effectiveness when selection stress is high, thus increasing variability within the genome of the stressed species.Bacteria have been observed cranking up the rate of mutation in response to stress ecologies in the lab, and observations outside the lab have vaerified it in bacteria and multicellular life. Fully 3/4's of zygotes (fertilized eggs) don't make it past the first few weeks after conception. Afterwards the incidence of miscarriage decreases with time up to birth, and all such miscarriages show some incompatibility with development into a living, breathing human.As this usually does not impair the parents from attempting another reproduction experiment the effect on the population as a whole is small: we still produce too many babies to replace the existing population.Enjoy.

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we are limited in our ability to understand
by our ability to understand
Rebel American Zen Deist
... to learn ... to think ... to live ... to laugh ...
to share.

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• • • Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click) • • •

Sorry, I was only kidding about the Ronda bit. I'll try to cut that out so as not to cause you unnecessary explanation. Don't let my mum hear that.

quote:

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Phylogenetic (Cladistic)/ Evolutionary / Darwinian species

​

A group of organisms that shares an ancestor; a lineage that maintains its integrity with respect to other lineages through both time and space. At some point in the progress of such a group, members may diverge from one another: when such a divergence becomes sufficiently clear, the two populations are regarded as separate species. Subspecies as such are not recognized under this approach; either a population is a phylogenetic species or it is not taxonomically distinguishable.

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How does one go about making that distinction. Is it one of those "you know it when you see it a gazillion times" things.Asked to quickly; you got it.Incipient: My word for the day.Your model is the model of evolution that I understand. I'm guessing I need give more credence to Percy to be less glib.Thank you

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Genesis 2
17 But of the ponderosa pine, thou shalt not eat of it; for in the day that thou shinniest thereof thou shalt sorely learn of thy nakedness.
18 And we all live happily ever after.

Thanks lyx2no2, But it turns out to be a serious question - not every male gets to mate with the cheerleader, but they do end up (usually) mating with someone they (may find more) attractive. This results in greater diversity than would happen if only alpha male\female organisms mated. Species that do have alpha only mating usually are small groups which can form new cliques, erm, packs. And I'm sure she already knows. Maybe fonda her "Help, Help me Ronda" days ... That's where the beauty of combining it with the 98% similarity metric comes in. For instance, we can look at the fossil record of Pelycodus: Here we see a series of arbitrary speciation events along the red lineage, places where there is sufficient difference from the ancestral population to mark this as a new species. Yes, we also see three branches off from the red lineage, branches that fairly quickly diverge from 98% similarity, thus confirming speciation, and in the top one we see a period where it could go either way before reaching that limit. That's the period of incipient speciation in this example.At this level evolution could reverse and the two populations recombine into one single population.Enjoy

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we are limited in our ability to understand
by our ability to understand
Rebel American Zen Deist
... to learn ... to think ... to live ... to laugh ...
to share.

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• • • Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click) • • •

Lyx2no can be at least partially right, one mechanism of DNA repair during replication is 'mismatch' repair, which as the name implies is based upon finding mismatches between bases on complementary strands.And of course the obligatory wiki link, for more information.TTFN,WK

Hey Wounded King,Thanks for the information. Wouldn't this also be a way for recessive genes to be replicated? Damaged dominant repaired from undamaged recessive - some intermediate merging?Or am I confusing things.Enjoy

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we are limited in our ability to understand
by our ability to understand
Rebel American Zen Deist
... to learn ... to think ... to live ... to laugh ...
to share.

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• • • Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click) • • •

Hi, RAZD. I think the mismatches Wounded King is talking about are mismatches on a single chromosome (which is made up of two complementary strands forming a double-helix). When the two chains of the double-helix don't complement each other, they don't anneal or coil properly, and a repair mechanism is initiated.Since dominance/recessiveness describes the relationship between an allele and its counterpart on the homologous chromosome, this process should be independent of dominance/recessiveness.

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-Bluejay/Mantis/ThylacosmilusDarwin loves you.

Hi Razd,Bluejay has it right, I was talking about the 2 complementary strands making up 1 DNA double helix rather than 2 distinct copies of a gene. There is a mechanism which allows for what you describe, it is called gene conversion and it does involve mismatch repair. During recombination, which can occur when homologous stretches of DNA become aligned as in meiosis, mismatch repair mechanisms can cause non identical stretches to become identical leading to the effective copying of a stretch of genetic material from one chromosome to the other.TTFN,WK