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Author Topic:   Is Reproductive Success the Gold Standard?
RAZD
Member (Idle past 1406 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 5 of 20 (496952)
01-31-2009 5:05 PM
Reply to: Message 1 by lyx2no
01-31-2009 12:41 PM


the long answer
Thanks for you confidence, lyx2no2,
... pretending to ask questions when they're really just trying to trip up the pros.
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:
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!
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.
My only understanding was that "specialization" (sorry, totally goofed that) is defined by sexual separation (which makes me and Ronda Kalowinski separate species).
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.
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.)
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:
quote:
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.
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.

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.


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

This message is a reply to:
 Message 1 by lyx2no, posted 01-31-2009 12:41 PM lyx2no has replied

Replies to this message:
 Message 10 by lyx2no, posted 01-31-2009 7:14 PM RAZD has replied

  
RAZD
Member (Idle past 1406 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 9 of 20 (496981)
01-31-2009 6:52 PM
Reply to: Message 7 by NosyNed
01-31-2009 5:32 PM


Re: DNA repair and selection
Hey Ned,
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.
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.
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.
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.

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.


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

This message is a reply to:
 Message 7 by NosyNed, posted 01-31-2009 5:32 PM NosyNed has not replied

  
RAZD
Member (Idle past 1406 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 11 of 20 (496998)
01-31-2009 8:42 PM
Reply to: Message 10 by lyx2no
01-31-2009 7:14 PM


Re: "Gold Standard of Genetic Fitness" Much Better
Thanks lyx2no2,
Sorry, I was only kidding about the Ronda bit. I'll try to cut that out so as not to cause you unnecessary explanation.
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.
Don't let my mum hear that.
And I'm sure she already knows. Maybe fonda her "Help, Help me Ronda" days ...
How does one go about making that distinction. Is it one of those "you know it when you see it a gazillion times" things.
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.
Asked to quickly; you got it.
Incipient: My word for the day.
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

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.


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

This message is a reply to:
 Message 10 by lyx2no, posted 01-31-2009 7:14 PM lyx2no has replied

Replies to this message:
 Message 16 by lyx2no, posted 02-05-2009 3:35 PM RAZD has replied

  
RAZD
Member (Idle past 1406 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 13 of 20 (497130)
02-01-2009 9:08 PM
Reply to: Message 12 by Wounded King
02-01-2009 6:52 PM


Re: DNA repair and selection
Hey Wounded King,
Thanks for the information.
... based upon finding mismatches between bases on complementary strands.
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

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.


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

This message is a reply to:
 Message 12 by Wounded King, posted 02-01-2009 6:52 PM Wounded King has replied

Replies to this message:
 Message 14 by Blue Jay, posted 02-01-2009 10:57 PM RAZD has seen this message but not replied
 Message 15 by Wounded King, posted 02-02-2009 8:54 AM RAZD has seen this message but not replied

  
RAZD
Member (Idle past 1406 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 17 of 20 (497739)
02-05-2009 10:17 PM
Reply to: Message 16 by lyx2no
02-05-2009 3:35 PM


Re: Not There Yet.
Hey lyx2no2,
Whee! I get to marry a cousin.
There's a series of jokes that all have the pattern "you may be a redneck if ..." (the term "redneck" implying ignorant country bumpkin with sunburned neck from long hours of hard field work), and one of my favorites is "you may be a redneck if you get married for the third time and still have the same in-laws"...
I’m not sure what “it” is, yet. “It” refers back to this entire:
"IT" is the division of a parent population into separate daughter populations that are no longer sharing genetic material by breeding.\
The question is whether reproductive separation is sufficient to declare speciation. So the idea is to compare the degree of similarity between the two branches to see if there is sufficient divergence to match the assumed level for arbitrary speciation. You have the same amount of difference, but in space instead of time.
But what does “when such a divergence becomes sufficiently clear” mean? How is “sufficient difference” determined? What do the little, black, horizontal bars in the image represent? Who is John Galt?
John Galt had the opportunity to drink perfect coffee.
The black horizontal bars represent the variation in the population at each specific level, with thicker bars for more numbers in that size - like a normal distribution of variation of a trait in any population.
How does one calculate the 98% similarity with an extinct species? I’m assuming, here, that one looks at some portion of a gene ...
That's why I prefer "traits" to "genes" - traits are seen in the visible parts of the fossils, the result of gene expression, rather than the gene itself. This is also more important for evolution, as evolution is based on selection of the phenotype - the expressed genes combined with the development of the organism.
When comparing fossil skeletons you can compare proportions of bones, size, distribution, etc. without needing to refer to the actual genes that led to such differences.
Are they comparing the ratios of all those little measurements they seem to be continually making with their calipers instead?
Yes, indeed. Well done. A little known aspect of paleontology is the exhaustive comparative anatomy that goes into cataloging species, variations in the species and why scientists feel they have found a "new" species.
Yes a lot of it is subjective, but the issue is consistency. Some people are "lumpers" - grouping a lot of variation into a small set of species - while others are "splitters" - dividing the variations into lots of species. Lumpers and splitters are each internally consistent, so they end up with the same overall pattern, just with a different number of nodes along the way.
Enjoy

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.


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

This message is a reply to:
 Message 16 by lyx2no, posted 02-05-2009 3:35 PM lyx2no has replied

Replies to this message:
 Message 18 by lyx2no, posted 02-05-2009 11:06 PM RAZD has replied

  
RAZD
Member (Idle past 1406 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 19 of 20 (498345)
02-09-2009 8:29 PM
Reply to: Message 18 by lyx2no
02-05-2009 11:06 PM


Re: There
Yep.
... about snails, which I believe he worked with.
Extensively, this article shows evolution at a snails pace:
http://www.hno.harvard.edu/...997/01.09/SnailsCaughtinA.html
Enjoy

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.


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

This message is a reply to:
 Message 18 by lyx2no, posted 02-05-2009 11:06 PM lyx2no has not replied

Replies to this message:
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