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Author Topic:   Definition of Species
RAZD
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Posts: 19842
From: the other end of the sidewalk
Joined: 03-14-2004
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Message 63 of 450 (541063)
12-31-2009 12:44 AM
Reply to: Message 41 by herebedragons
12-22-2009 2:13 PM


Re: for herebedragons - speciation, definition first, discussion second
Hi herebedragons, I'm going to pick up on some older points.

Although the most popular and widely excepted definition seems to be the Biological species concept, ...
... but both speciation and reproductive isolation remain problematic issues. "Reproductive isolation", widely considered an essential ingredient in defining the word species, is itself vaguely and inconsistently defined. Exactly when does reproductive isolation occur? what are the actual mechanisms that bring it about? is geographic isolation enough to develop reproductive isolation? what does “potentially” interbreeding individuals actually mean? etc. Truly “reproductive isolation” is quite ill defined.

In fully developed reproductive isolation interbreeding is impossible, so this is not problematic. When you have behavioral or geological isolation you have the beginning of isolation, where genetic incompatibility can occur and not be selected against. It's not a sudden occurrence.

Then throw into the mix hybridization.

See previous reply about variations in hybrid viability, which is also an ongoing process in some instances.

The author gave an analogy that I think clearly illustrates the problem and also the problem of presupposing or historically considering a form to be a separate species despite there ability to interbreed as are the Spanish sparrow (P. hispaniolensis) and the house sparrow [P. domesticus].

I have seen some bad analogies in my time, but this one is rather insulting to scientists. Aside from the issue that a species are generally not defined in relation to another species (exception: symbiology co-evoution, which includes the co-evolution of multicell organisms and the bacteria they carry, such as stomach that aid digestion - termites are termites because their gut has bacteria that digests wood cellulose), the implication that decisions like this are based on such simple whimsy is down-right false. There may be subjective elements involved, but the amount of detail that is documented before a new species is declared is voluminous in details of traits compared and relative differences noted - there is more to it than the observation that bone "A" is longer in specimen "B" than in specimen "C".

You realize that your "authority" is proposing a "new" theory on "On the Origins of New Forms of Life" yes? Interesting theory, but I predict it will be of marginal value in only some instances - instances where hybrids can form and speciation has not fully occurred, so this is really mixing up the breeding population after a short separation that develops some distinctive new traits. Once reproductive isolation occurs we are back in the same-old same-old. This is not a new concept, and several people have suggested similar ideas.

Message 43: My apologies, Mr. Jack, but what consitutes a "credible" source as opposed to a "crank website"? I am avoiding "creationist" sites as they are "crank" or "bogus". But this was not a creationist site.

It's a crank website because it promotes a personal hypothesis and apparently is the only source for this hyposthesis. Such things occur in all sciences, and it is easy for a person not educated in the science to be unaware of the basic problems and ramifications of these "new" hypothesis.

I only found one site that discussed this theory in comparison to the normal paradigm in biology:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2556406/
Three ambitious (and rather unorthodox) assignments for the field of biodiversity genetics, by John C. Avise (this hypothesis is only covered in the beginning sections, and is mostly considered as a means of testing the normal paradigm). It tells you how you can test for the validity of the hypothesis and what you should see in the genetic records.

It seems to me the concept of species is very illusive and there is no “one size fits all approach”. In addition, I’m not sure it has any value in the real world other than for our convenience in discussing different animals. IOW when I say ‘zebra’ you know I am talking about an animal that lives in Africa and has black and white stripes and when I say ‘horse’ you know I am talking about a domesticated animal that is primarily used for human recreation. Whether they are clearly distinct species may be irrelevant. The problem with a statement like that, from an evolutionist’s point of view, is that if a species distinction is irrelevant, that kinda makes speciation irrelevant too, since after speciation occurs the results would be irrelevant.

Not when we have reproductive isolation. Horses and zebras can interbreed (see zorse) just like horses and donkey, and with similar infertility as a result. Rather obviously these infertile hybrids are not going to be bringing new "stabilized" traits back to either horse or zebra population, and thus the time when this could be a factor in equid evolution has already passed for these species, and we have distinct different species - horse, zebra, donkey, quagga.

I have been doing some reading about DNA sequence analysis and feel there is a lot of promise to resolve some of these problems and give us a clearer picture of lineage and thus history, but I have a feeling evolutionists (specifically gradualists) and creationists alike are going to be disturbed by the results. Any other input on DNA sequencing would be helpful as I know very little about the terminology or theory behind it.

Or they will welcome the new additional data that by and large has verified to an amazing extent the tree of life pattern that has been derived from detailed morpological analysis, with some rearrangements in lineage being inevitable, but the overall pattern still holding. Remember that this is already done for some of the branches, such as humans, chimps and other apes, where the genomes are known for the different species, and a cladistical analysis based on the genetics results in a very similar cladistic analysis of the hereditary relationship previously developed through analysis of the fossil record.

Remember that the fossil record and the genetic record are both tests of the concept\hypothesis\ToE, that evolution (the change in frequency of hereditary traits in breeding populations from generation to generation) and speciation (the division of breeding populations into reproductively isolated daughter populations) are sufficient to explain the diversity of life as we know it, and thus when they give similar results this is validation of the theory.

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 ...
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This message is a reply to:
 Message 41 by herebedragons, posted 12-22-2009 2:13 PM herebedragons has not yet responded

  
RAZD
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Posts: 19842
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 5.9


(1)
Message 66 of 450 (541938)
01-06-2010 10:50 PM
Reply to: Message 64 by herebedragons
01-06-2010 11:46 AM


Re: Speciation discussion
Hi herebedragons,

I'll have to get back to you tomorrow, but just a quick note:

Example: http://www.fossil-museum.com/fossils/

Harun Yahya is a convicted fraud, not someone I would trust with the truth. His "atlas of creation" shows a fishing lure as an example of a living bug.

http://richarddawkins.net/articles/2833

One needs to be skeptical of sources that seem to provide the evidence you want while ignoring the rest of the story.

Tomorrow we will get back to species.

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 64 by herebedragons, posted 01-06-2010 11:46 AM herebedragons has responded

Replies to this message:
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RAZD
Member
Posts: 19842
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 5.9


Message 69 of 450 (542144)
01-07-2010 9:30 PM
Reply to: Message 64 by herebedragons
01-06-2010 11:46 AM


Re: Speciation discussion, expectations and reality
Hi again herebedragons, I have some time now to concentrate on the issue of speciation.

Thanks for link to the Berkley series. It is very well done. I do appreciate how they clearly distinguish between what is theory, what are predictions based on the theory and what is actually observed. This is not always done in evolutionary literature.

Frankly, I have never had a problem distinguishing the two, nor do I think any of my classes (back through high school) ever conflated them. I have always found this assertion by creationists to be curious, almost as if they were creationists because they were victims of bad education.

But yes, I think Berkeley has the best website on the internet to explain evolution in clear discrete articles.

What I've learned so far about species and speciation has been pretty unimpressive (and by unimpressive, I mean in an evolutionary sense - there are some truly remarkable things to learn about our world). I am looking for observations that I believe are clues to larger scale changes. I know you will be quick to point out that to see those types of changes we need to look at the fossil record as our time frame for observation is miniscule compared to evolutionary time scale. But what I find appears to be much more like variations within a species.

Before we go there, let's explore why you think there should be "larger scale changes" - how much "larger" and how do you define the scale of change? Certainly there is no known "other mechanism" to cause change, regardless of size, so we are left with normal evolutionary mechanisms.

Take the species Brassica oleracea for example. I was shocked when learned that Kale, Broccoli, Cabbage and a dozen other disgusting vegetables were not just in the same family or even genus, but the same species! Just different cultivars. There is tremendous variation in these plants and the only thing they seem to have in common is they are nasty tasting lol. Is that truly evolution?

And of course, dogs and even horses exhibit drastic amounts of variation within species boundaries. It is duly noted that all above mentioned examples are due to human breeding and cultivation, not natural processes. But also note that human breeding and cultivating is a intelligent, directed process - not undirected and random. Can an undirected, random process create so much diversity?

Personally I doubt that the extreme variations selected artificially would be found in nature to produce the same degree of variety at any one time, but what this shows is just how much variation can happen in short periods of time (geologically speaking). We can take this as a metric for how much time is needed as a minimum to go from {average\original condition} to an {extreme condition}. In fact I have proposed doing this on the Dogs will be Dogs wil be ??? thread.

We can also see where selection for one particular trait can lead to some rather interesting developments in a fairly short period of time:

http://cbsu.tc.cornell.edu/ccgr/behaviour/History.htm

quote:
The silver fox (Vulpes vulpes) is taxonomically close to the dog (Wayne, 2001) but although reared in captivity, they had not been domesticated previously. Under standard farm conditions foxes normally exhibit distinct patterns of aggressive and fear-aggressive behavior to humans. Dmitriy Belyaev, and colleagues hypothesized that a selection of farm foxes for less-fearful and less-aggressive behavior would yield a strain of domesticated fox (Belyaev 1969, 1979; Trut, 1999).

Selection for tame behavior was started at the Institute of Cytology and Genetics (ICG) in Novosibirsk, Russia in 1959 with 130 farm-bred foxes that demonstrated the least avoidance behavior towards humans. Subsequently, only the tamest individuals in each generation have been allowed to breed, while at the same time a deliberate effort was made to avoid inbreeding (Trut, 1999, 2001; Trut et al., 2004). The tame population developed relatively fast in response to selection - with 18 percent of foxes from the tenth generation demonstrated extremely tame behavior. Little behavioral variation was observed by 1985 and thereafter (Trut, 1999, 2001; Trut et al., 2004).


So in a fairly short period of time, selection only on the basis of tame behavior led to a rapid increase in tame behavior within the (allowed) breeding population. But this simple statement doesn't tell you what else occurred:

https://www.youtube.com/watch?v=enrLSfxTqZ0

Of course many of those traits don't appear in fossils, so it is hard to correlate this with the history of dogs without having additional evidence (such as pictographs of dogs) that similar changes occurred. Note that many of these trait changes are also what we see in cows and pigs and cats, and other domesticated animals.

This is the area covered by evolutionary development - evo-devo - a fairly new field, where changes in hormones or environmental chemicals can affect the way organisms develop from fetus to adult. See also thalidomide.

This is important, because natural selection operates on the phenotype - the 'as-built' form of the individual - rather than the genotype. Anything that affects the phenotype that is not part of the genotype can thus be important for selection processes, and the genetics of the selected individuals are more or less along for the ride (neutral drift).

Some people feel that evo-devo is responsible for the more dramatic changes in evolutionary history (including possibly the first formation of vertebrates).

Their research doesn't discredit the evolution of the horse, but sheds light on the amount of diversity that has occurred within a species over time. Analysis of lineages based on good old fashioned morphology is questionable.

Curiously the evolution of horses has seen some re-evaluation based on morphology that shows more variation than had been supposed 50 years ago.

http://www.flmnh.ufl.edu/natsci/vertpaleo/fhc/Stratmap1.htm

Note that the groupings show are the different genera, with species being even more varied (and variations within species another level of variation).

Their research doesn't discredit the evolution of the horse, but sheds light on the amount of diversity that has occurred within a species over time.

Now we can argue that the morphological analysis centers on the average of the population in the record, and that all this new information means, is that there is a wider circle around that average position at any point in time. Then as we shift through the time layers to the next set of fossils we see the same average plus wider circle around that average position, and thus are more likely to have clear overlaps from one layer (age) to the next layer (age) making the transition from one to the other even more likely.

This is similar to the Pelycodus example in Message 57 where the overlap in sizes from layer to layer show clearly the transition from one population group to the next to the next.

So we see that a fair degree of variation can exist in a breeding population at any one time, and we see that a fairly remarkable degree of change can occur in a breeding population subject to constant selection pressure in a fairly short period of time.

Then we can compare this to the degree of change seen in the fossil record to see if this rate of variation and change are sufficient to explain the change from one age layer to the next age layer in a population of fossils that share morphologically homologous structures.

If this is sufficient to explain the fossil evidence then no "larger scale changes" are necessary. Do you agree, or do you want to see more change spread out over more time?

I know you will be quick to point out that to see those types of changes we need to look at the fossil record as our time frame for observation is miniscule compared to evolutionary time scale.

Certainly to see more change than is observed in these examples of rapid evolution seen within our minuscule time frame. Most evolution is your ordinary "unimpressive" kind as there is no severe selection pressure and what selection pressure occurs is usually not constant but varying, resulting in a "staggering drunken walk" to get from point "A" to point "B" (and no clear reason to go there).

How much more change is needed?

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 64 by herebedragons, posted 01-06-2010 11:46 AM herebedragons has responded

Replies to this message:
 Message 70 by Wounded King, posted 01-08-2010 2:51 PM RAZD has acknowledged this reply
 Message 72 by herebedragons, posted 01-22-2010 11:15 AM RAZD has responded

  
RAZD
Member
Posts: 19842
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 5.9


Message 75 of 450 (544005)
01-22-2010 7:56 PM
Reply to: Message 72 by herebedragons
01-22-2010 11:15 AM


Re: Speciation discussion, mutations, possibilities and opportunity
Hi again, herebedragons.

Now it's my turn to apologize for taking so long to respond.

No need, this pace suits me, and it allows for digestion of information before proceeding to the next level, and better understanding of your concerns.

How much more change is needed?

Needed for what? To convince me that the ToE is accurate and is the best explanation for life on this planet? To convince me that creation is a myth? Or that God doesn't exist? Or simply to convince me that organisms change over time?

I am convinced that organisms change over time. It's obvious they do. What I am not convinced of is the extent of change. Fish --> Amphibians; Theropods --> Birds; Chimps --> Humans.
...
But I am having a hard time taking observed evolution and extrapolating that into the kind of changes mentioned above.

And so we shall endeavor (eventually) to focus on this "macro" level of change, noting that macroevolution occurs above the level of (ie after) speciation, to show that evolution can explain the diversity of life as we know it, including the transition from fish to amphibian, therapod to bird, or ancestral apes into chimps and humans. We may need to move to another thread to discuss this (perhaps the Dogs will be Dogs wil be ??? thread as a start).

The rest will be for you to decide, however please note that I am a Deist, not an atheist.

Now be honest, just based on what we've discussed so far would it be enough to convince you if you were skeptical?

The observed process of evolution -- the change in the frequency of hereditary traits in breeding populations from generation to generation -- is the foundation. We agree that this occurs, and now we can build on that foundation.

The next stage is to show how this leads to speciation (which will return us to the topic here).

One of the major things I am having the hardest time wrapping my mind around is the idea of random mutations being the source for new biological innovations.

Let us consider the source of mutations first then, and their role in the evolutionary process.

The major source of mutations is imperfect replication: during reproduction the DNA of the parent is imperfectly replicated in the cells for the offspring. This occurs in every cell reproduction, but is most relevant to evolution in the reproduction process, the formation of the germ (sperm and egg sex) cells or the bud (asexual) cells. Again, this is an observed process in all known life forms.

I picture a "random mutation generator" functioning much like a program they use in movies to decode passwords, trying thousands of combinations until one works. Maybe this isn't very realistic, but still, there would be literally thousands, maybe hundreds of thousands, of mutations that could occur until by chance it stumbles upon the right mutation that works.

This is a common argument from improbability, however there are a couple of problems with it, not least of which is that there can be millions of potential solutions -- different mutations in different parts of the DNA that can result in usage of the substrate provided. Another is that the target is not a random chemical, but a known organic compound (amino acid iirc), and there may be hundreds of different ways to utilize this particular organic compound. All evolution needs is A way to utilize the compound, and the method found does not need to be the most efficient either, just functionally superior to not using it (resulting in a net increase in energy from the compound to the organism). Further mutations can refine the process and improve the efficiency.

In this one case we are talking about some 400 generations and many thousands of descendant organisms from a single parent organism, each with many mutations, so there are a lot of opportunities involved. How many times do you need to throw 10 dice to get all 6's? The probability of it occurring increases with the number of throws. It could happen on the first throw or the 400th (such is the nature of probability).

This probability seems small if only one specific mutation is required at one specific location, however if all that is needed is one specific DNA combination to make use of the second substrate, there are many ways to derive that specific combination by various recombinations (mutations) of existing DNA. With each additional possibility the likelihood of one of those being found increases dramatically. How many times do you need to throw three dice to get three 6's?

Additionally, I saw no mention of any other mutations that occurred during the study. The only one that was noted was the metabolic pathway. The law of probability would dictate that other mutations are just as likely to occur, even when you take selection into account. I am sure neutral mutations did occur, but there must be other beneficial mutations that could have occurred instead of, or in addition to, the metabolic pathway mutation. When the experiment is repeated, you should see other randommutations occuring.

Indeed. As I recall, the mutation at the 400th generation made use of a previous neutral mutation, and only those populations with that particular neutral mutation could evolve to use the substrate. Neutral mutations are the most numerous in surviving organisms (the deleterious ones that kill organisms having done their work, and being largely unnoticed by the absence of cells that don't form).

Quite often mutations are neutral in their original environment, but then are beneficial or deleterious in a new one.

Another problem I have is that in nature the environment would not likely be stable enough to give the organism time to come up with a mutation randomly. The levels of the food source would fluctuate and other environmental forces would compete for the organisms "attention".

Organisms do not "come up" with mutations. Do not think of mutations as having to occur, rather that they happen, and that whatever happens provides an opportunity to be useful, neutral, or harmful.

Ecologies usually fluctuate around average conditions, and thus you can have repeated occurrences of ecologies where specific mutations may provide an opportunity for benefit to the organisms that have the mutation, but which are neutral in intervening periods. This would increase the time for such mutations to be of benefit to the breeding population, so in the wild it may take more than 400 generations to have an opportunistic mutation.

All in all, the probability that this pathway evolved randomly seems mind boggling to me. And that's just a fairly simple (biologically speaking) change.

And yet, experiment after experiment after experiment confirms that such opportunistic mutations do occur, and that they occur in sufficient frequency that they can be observed and documented. That something is "mind boggling" is not any criteria on which to base a scientific conclusion (else much of physics and chemistry would be discarded), and it can be due to ignorance of the actual possibilities, or just being uninformed. Nature cannot be expected to be expected.

A more likely explanation would be that the information for the new pathway was already contained in the genome and the change in environment caused it to be turned on like a switch.

More likely? Then why does it take (a) 400 generations for one E. coli. to develop the mutation that (b) requires a previous neutral mutation, and (c) does not occur in the millions of other E. coli. organisms that are part of the study? What about the ones that fail to find a mutation -- they would have had the same "pathway ... already contained in the genome" and they are subject to the same "change in environment" to cause "it to be turned on like a switch" would they not, -- if this were the case? A single organism succeeds in surviving on the second substrate, but the millions of others somehow can't find that very same previous pathway locked in their DNA? Remember that in science the best explanation is the one that explains all the evidence -- the failures as well as the successes.

I would be interested to know if the E. coli that had developed the new pathway could go back to using the original pathway. Would it have to re-evolve by random mutations? Or does it still exist in the coding?

It is possible for point mutations to reverse (undo), but in general evolution does not work in reverse. Similar paths may evolve, but are not likely to repeat previous systems. As an example, there are also experiments done where an existing path is deactivated, and a new path is evolved, with a different efficiency than previous, but still able to derive a net benefit. See Irreducible Complexity, Information Loss and Barry Hall's experiments for an example, one that also involves an "irreducibly complex" mechanism, and where the new system is less efficient than the original.

The variation in dog breeds and the B. oleracea species would be another indication of this. There are large amounts of morphological differences and yet very little genetic distance. This would indicate that the information was already contained in the DNA and selection merely changed what genes were expressed.

Or that small differences during development can have significant effects on the fully developed organisms. What was selected was different levels of adrenaline in the parents, a hormone that directly affects development in the womb.

Again, this took several generations to realize the result, it did not happen in the second generation, because natural levels of adrenaline was higher in all original foxes.

First of all, the trait for tameness did exist in the silver fox population (they selected for the tamest individuals - although in this case tameness is a relative term).

The trait for "tameness" did not exist. None of the wild foxes behaved in a tame manner. There were different levels of aggressive behavior, and they selected for the least aggressive.

Secondly, after they managed to tame the population (domesticate) they exhibited many of the same complementary traits that dogs exhibit. Is this a coincidence? What are the chances that this was random? It seems highly, highly improbable to me. Ancestry could explain it, but enough genetic variation should have accumulated to make it somewhat less likely that they would exhibit similar complementary traits.

Interestingly, this same pattern of coloration, floppy ears, and behavioral changes are also seen in other domesticated mammals - cats, pigs, horses, cows, sheep, etc. In all these cases the measured level of adrenaline is lower in the domestic stock than in the wild stock, and thus the explanation, that the different levels of adrenaline during development of the fetus, is a more likely explanation for all these instances, rather than some archaic ancestral preserved segment of DNA, that somehow miraculously survives in all these species from their remote common ancestor. In other words, you will need to already accept the macroevolution of mammals from a common ancestor in the distant past to propose that this mechanism explains the changes observed via preserved DNA. You would also, it seems to me, need some mutation mechanism to activate it, or it would remain hidden.

Again, if we want to continue to discuss the macro aspects of this, we should be moving to another thread (perhaps the Dogs will be Dogs wil be ??? thread before moving on to the further macroevolution mentioned above).

Let us conclude with mutations first eh?

So we have mutations, randomly occuring in populations providing some organisms with occasional beneficial opportunities, but the vast majority being neutral or not beneficial, ...

... or we have some unknown mechanism that preserves some unknown unused archaic ancestral DNA for millions of generations until it is needed by one out of thousands of equally deserving descendant organisms?

... the information ... was already contained in the genome and the change in environment caused it to be turned on like a switch.
This would indicate that the information was already contained in the DNA and selection merely changed what genes were expressed.

The DNA can be (and has been) compared between the original single E. coli. organism and the descendent ones that make use of the second substrate, and the result is that there are sections in the descendents that did not exist in the original: by what magic do these new segments appear out of their ancestral hiding place? How does this "switch" work?

You claim that this "hidden DNA" explanation is "more likely" and I have trouble seeing how it is even possible.

I am convinced that organisms change over time. It's obvious they do. What I am not convinced of is the extent of change.

For the purpose of this thread, we will need to show the degree of change necessary to result in speciation, the division of a parent population into reproductively isolated daughter populations, by the process of evolution. This occurs through mutation and natural selection operating on the sub-populations in different ways, and to understand this we need to understand how mutation operates in populations to provide opportunities.

We have seen an example of one mutation occurring in 1/400 generations in 1/1,000,000's of individuals being beneficial to the organism and its descendants. We have also seen selection of different levels of hormones in a population having an effect on the morphological development of following generations in a fairly rapid (relatively speaking) pace.

The first involves mutation, the second involves selection, and together they accomplish more than either can alone.

Enjoy.

Edited by RAZD, : clrty

Edited by RAZD, : first throw.

Edited by RAZD, : 3-6's


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 72 by herebedragons, posted 01-22-2010 11:15 AM herebedragons has responded

Replies to this message:
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RAZD
Member
Posts: 19842
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 5.9


Message 77 of 450 (544014)
01-22-2010 8:36 PM
Reply to: Message 76 by Coyote
01-22-2010 8:20 PM


selection and mutation vs mutation alone
Hi Coyote,

The analogy I prefer is throwing 10 dice and keeping those with sixes, while rolling only those that are not sixes. You will have sixes on all ten dice in minutes.

Yes, as that shows the power of selection combined with mutation, however at this point we are only talking about the possibility of mutation, so selection is not involved yet.

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 76 by Coyote, posted 01-22-2010 8:20 PM Coyote has not yet responded

  
RAZD
Member
Posts: 19842
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 5.9


Message 81 of 450 (546316)
02-09-2010 10:17 PM
Reply to: Message 78 by herebedragons
02-08-2010 11:08 AM


Re: mutations, possibilities and opportunity
Hi again herebedragons,

I probably shouldn’t have responded the way I did, but I felt the question “how much more change is needed?” was a bit condescending and begged a ”needed for what?” reaction. I do feel an obligation to accept evidence from observation, what I do not feel obligated to is interpretation of those observations.

We need to remember that the focus of this topic is the definition of species rather than a generic ramble about evolution. We started to get offtrack with your claim:

Message 64: What I've learned so far about species and speciation has been pretty unimpressive (and by unimpressive, I mean in an evolutionary sense - there are some truly remarkable things to learn about our world). I am looking for observations that I believe are clues to larger scale changes.

And now we seem to be sidetracked with the issue of how much change is necessary.

Message 72:
How much more change is needed?

Needed for what? To convince me that the ToE is accurate and is the best explanation for life on this planet?

Let's look at what type of change is needed for speciation first. I would agree that the amount of change necessary for speciation is unimpressive: as noted in Message 62 there is very little difference between the varieties of asian greenish warbler, yet we have a situation where two varieties don't interbreed. These varieties are all descended from a single ancestral population, so if we did not have the intermediate varieties we would have a clear unambiguous speciation event.

Therefore large change is not needed for speciation to occur, and the issue of larger change is not really on topic for a thread on the definition of species.

To discuss larger change then I think we need to move to another thread.

Message 62: You can think of the "Theory of Evolution" as the hypothesis that evolution - the change in the frequncy of hereditary traits in breeding populations from generation to generation - and the process of speciation - the division of a parent population into two or more reproductively isolated daughter populations - is sufficient to explain (a) the fossil record, and (b) the genetic record. As such the fossil record and the genetic record become tests of the theory, tests capable of falsifying the theory.

If you want to discuss how these can be applied to the fossil record in order to judge the validity of the evolutionary explanation, another of my threads addresses this in a different format:

Dogs will be Dogs wil be ??? - this uses the variation within the dog species as a metric to compare the variation between different fossil species, assuming that the variation seen in dog species is the maximum that can occur in a species, and then seeing if the difference between two or more closely related (in time and space and morphology) exhibit more or less variation than we see in dogs.

There we can explore the evidence that shows a dog-like ancestral organism evolving into the modern horse, and see if that shows how larger changes occur.

I understand that the rate of error in DNA reproduction ...

This and Message 79 should probably be a new thread.

I don't mean to put you off, just trying to maintain the topic of this thread.

Enjoy.


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This message is a reply to:
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RAZD
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Message 86 of 450 (569801)
07-23-2010 8:53 PM
Reply to: Message 83 by barbara
07-23-2010 1:11 PM


Re: Speciation discussion, expectations and reality
hi barbara, thanks for the questions.

I don't know how science can build their models of speciation since humans have directly or indirectly affected the course of natural evolution.

Scientists observe that a parent population divides into two sub-populations living in different ecologies and then sees that these daughter populations become incapable of interbreeding.

Thus speciation has occurred.

Humans have directly changed the entire globe's landscaping to fit their needs and all species had to evolve with it.

The ecologies within the oceans are largely untouched by direct human intervention, and a large amount of human effect is no different in the kind of change induced than what occurs naturally (extra CO2 in exhaust? similar to past levels?) -- it may be more a matter of degree of change than the type of change.

The only place I can think of where a type of change is induced by humans is chemical pollution.

The only real effect likely to be observed is that ecologies are changed more rapidly by human intervention, and thus the rate of evolution may be different.

Enjoy.


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RAZD
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Message 131 of 450 (570824)
07-29-2010 12:12 AM


TOPIC
The last 50+ posts have nothing to do with the definition of species.

See Message 87 onward (in a downward spriral)


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Message 175 of 450 (572442)
08-05-2010 9:09 PM
Reply to: Message 157 by Big_Al35
08-05-2010 8:34 AM


Species Definition vs what matters (and why)
Hi Big_Al35,

Thanks for staying on topic, even if you are making a number of assertions from an under-informed base (not ignorant, but not fully cognizant either):

...I am not a paleontologist or biologist.

And a great way to learn is to ask questions. Hope this isn't too long ...

To the issue of "fish" and "shark" and any other commonly used layman's term for organisms, this is necessarily fraught with misconceptions and mistakes. Taxonomists use many multitudes of measured traits to determining homologous (by descent) versus analogous (derived independently) traits in the formation of trees of descent.

To your basic issue of species definition, there is no single definition that works. Even with DNA sequencing there will be problems, and as you point out, our knowledge of the DNA of fossils is ... slim to none.

But we can't just make up ad hoc species and lump these fossils under that category. It couldn't be defined as a species under any of our definitions anyway. We don't have access to the DNA, we don't know their behaviour and we can never know if they could interbreed. It has become an exercise in futility.

But this assumes that DNA knowledge is critical to determining different species: it isn't. It kind of seems that you want to include DNA in the definition of species, so that then you can claim that species cannot be determined without knowing the DNA. This is employing a logical fallacy in your approach.

The real question is: what matters?

Species labels are useful to human scientists to differentiate bits and pieces of information from the fossil record, from the genetic record, and from the world around us.

Let me introduce the concept of "lumpers" vs "splitters"

Lumpers put lots of populations of organisms into one lumped group and label that a single species, with a number of varieties (slightly different traits, theoretically able to interbreed.

Splitters divide up populations into many small groups and label each one a different species, while the next larger group, genus, incorporates other closely related species that may be able to interbreed but typically don't.

quote:
http://www.zoology.ubc.ca/~irwin/GreenishWarblers.html

Greenish warblers (Phylloscopus trochiloides) inhabit forests across much of northern and central Asia. In central Siberia, two distinct forms of greenish warbler coexist without interbreeding, and therefore these forms can be considered distinct species. The two forms are connected by a long chain of populations encircling the Tibetan Plateau to the south, and traits change gradually through this ring of populations. There is no place where there is an obvious species boundary along the southern side of the ring. Hence the two distinct 'species' in Siberia are apparently connected by gene flow.

Here we have between two and five species (if you're a splitter) and one species with five varieties (if you're a lumper), based on how much you count gene flow through the (small) hybrid zones.

Organisms are generally lumpers compared to humans, relatively unconcerned about what is or isn't a species (it's basically a them kind and us kind approach, although them kind can be broken up into eat this, avoid that, etc). You could call this the "organism definition" of species, and lump a lot of different organisms into big categories. This becomes highly unweildy when populations change from the "eat this" species to the "avoid that" species ... and back.

All the definitions we have of species have similar problems, and this leads to long discussions between lumpers and splitters.

But the point to keep in focus is that they matter to us as a means of describing groups of organisms, and how they fit into the broad scheme of things.

As far as evolution is concerned species is important for two reasons: (1) to define a discrete population (a breeding population) to monitor the process of evolution within the population, and (2) to define when speciation (the division of a breeding population into two or more daughter populations that become reproductively isolated from the others) occurs.

Let me introduce you to the concepts of "arbitrary speciation" and "non-arbitrary speciation" so you can see how this works.

In essence, "arbitrary speciation" occurs when a descendant population is no longer capable of breeding with an ancestral population, however this can end up with an awful lot of species definitions (especially if you are a splitter eh?) -- virtually every other generation. This would get pretty unwieldy very rapidly.

So an arbitrary speciation designation is normally made based on the descendant population at some point becoming as distinguishable from the ancestral population to the same arbitrary approximate difference as exists between two closely related species.

The changes accumulated in the descendant population are similar in degree to the differences between closely related species.

"Non-arbitrary speciation" occurs when two (or more) daughter populations become reproductively isolated from the parent population (as above) and each other, leading to different evolution in different ecologies, and reaching the point where interbreeding does not occur.

quote:
http://www.don-lindsay-archive.org/creation/pelycodus.html

The numbers down the left hand side indicate the depth (in feet) at which each group of fossils was found. As is usual in geology, the diagram gives the data for the deepest (oldest) fossils at the bottom, and the upper (youngest) fossils at the top. The diagram covers about five million years.

The numbers across the bottom are a measure of body size. Each horizontal line shows the range of sizes that were found at that depth. The dark part of each line shows the average value, and the standard deviation around the average.

The dashed lines show the overall trend. The species at the bottom is Pelycodus ralstoni, but at the top we find two species, Notharctus nunienus and Notharctus venticolus. The two species later became even more distinct, and the descendants of nunienus are now labeled as genus Smilodectes instead of genus Notharctus.

As you look from bottom to top, you will see that each group has some overlap with what came before. There are no major breaks or sudden jumps. And the form of the creatures was changing steadily.


Here we have a number of "arbitrary speciation" events, marked by the different species designations along the general trend from lower left to upper right. We also have a couple of instances when the breeding population divides into two groups with a horizontal gap between them, yet overlapping ancestral populations.

These divisions are non-arbitrary speciation events: the two daughter populations after a split are not interbreeding, and this results in the horizontal gap between them.

I have accessed the original article and made the following colored lines on the same basic data to emphasize what is going on:

We see the "drunken walk" of evolution within an overall trend, and if we draw a line down from the left end of Pelycodus trigonodus we see that it is outside the range of traits for Pelycodus ralstoni while a line from the right end up to the top is outside the range for Pelycodus jarrovi.

The divisions of populations like this is evidence of non-arbitrary speciation events in the fossil record even though we do not have DNA samples from any of these fossils.

The staggering along trend that accumulates differences over time, while maintaining overlaps with ancestral and descendant populations shows that arbitrary speciation depends on where you subjectively draw the line, but approximates the same degree of change as occurs between daughter species in non-arbitrary events.

The non-arbitrary events only occur in sexual species, as this depends on the (sexual) biological definition of species.

Arbitrary speciation events would still occur in asexual species, but where you make the differentiation depends on a subjective analysis of when the accumulated changes are sufficient to justify a new arbitrary label for a bunch of organisms in order to describe things.

And whether you are a lumper or a splitter.

Enjoy.


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This message is a reply to:
 Message 157 by Big_Al35, posted 08-05-2010 8:34 AM Big_Al35 has responded

Replies to this message:
 Message 177 by Big_Al35, posted 08-06-2010 5:20 AM RAZD has responded

  
RAZD
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Posts: 19842
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 5.9


Message 203 of 450 (572608)
08-06-2010 6:59 PM
Reply to: Message 177 by Big_Al35
08-06-2010 5:20 AM


Re: Species Definition vs what matters (and why)
Hi Big_Al35,

I think it's fair to say that species cannot be determined unless you know their DNA. All the other criteria for determining species can only give best guesses. Maybe DNA is also a best guess.

Thanks for not reading 90% of my post and misconstruing the rest.

We can absolutely determine that pelycodus divided into several different species during the time of the fossil chart ("The diagram covers about five million years."), because of the separation of breeding populations.

This is what is important.

The graphic does not show you where to define the arbitrary speciation events, as those are subjective, however it does show that evolution -- the change in frequency and character of hereditary traits in breeding populations in response to ecological opportunites -- is an ongoing process, and it shows that sometimes that process leads to parent populations giving rise to two or more daughter populations.

This is what is important.

Whether we give them names or not is immaterial to the fact that several speciation events are observed to have occurred, and the evolution is observed as a continual process over the time period covered.

Therefore evolution and speciation account for the diversity observed in this fossil record.

... unless you know their DNA. All the other criteria for determining species can only give best guesses. Maybe DNA is also a best guess.

Curiously, even knowing the DNA does not help, as all you are doing is adding another element to use in making a subjective determination of when arbitrary speciation occurrs -- the DNA changes by a certain amount (if you can measure it for extinct species, which makes it virtually useless for MOST species).

If the difference in DNA does not result in any apparent difference in observable traits nor in behavior nor in survival nor in breeding ... does it really mean you have a new species because x% (your subjective arbitrary measurement level for separating species) is different?

Curiously, we can agree that species classifications are highly subjective, often completely arbitrary, and subject to change, and yet still use these classifications for the study of evolution in particular and biology in general. This is because scientists agree on using the published classifications for contextual clarity, rather than creating confusion by everyone using their own subjective classifications. The classifications of species is not a simple short list, but one based on a thorough comparison of many traits, including every bone in a skeleton that can be measured and quantified.

And the only real "controversy" is whether we have a genus with several species or a species with several varieties, all descended from a common ancestral population in either case.

They are necessarily arbitrary classifications for ~99% of organisms, because we only know that there are two different species when a non-arbitrary speciation event has occurred.

That doesn't mean that species designations are not useful in describing populations of organisms.

It certainly does not mean that evolution -- the change in frequency and character of hereditary traits in breeding populations in response to ecological opportunites -- is not an ongoing process,

OR that speciation -- the division of a parent population into two or more reproductively isolated daughter populations due to different evolution in daughter populations living in different ecologies, and a reduction in gene flow between them -- does not occur.

We could do away with species classifications altogether and only use cladograms based on hereditary traits, and the results would be the same, it would just be more difficult to discuss without names for the cladogram branches.

Enjoy.

Edited by RAZD, : ing


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RAZD
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Message 209 of 450 (573339)
08-10-2010 11:02 PM
Reply to: Message 204 by Big_Al35
08-10-2010 8:18 AM


Re: Species Definition vs what matters (and why)
Hi Big_Al35, in addition to what others have posted let me add this:

But I understand how you guys operate now. Maybe you paleontologists and biologists have livelihoods and jobs at stake. It serves your purpose to keep the rest of us in ignorance. As long as DNA is considered arbitrary and a bit of a joke you can continue your fossil finding and your species discoveries. You can make all sorts of absurd claims of finding common ancestors, missing links, new discoveries etc...then when questioned you can claim that you never meant that at all. As no DNA is available for most species that have ever walked the earth no one can ever prove you wrong....eh?

Rather than the conspiracy theory you have just asserted, the alternative is that scientists realize the limitations of finding DNA for all the extinct species, and this is why they use alternative methods for determining hereditary traits (ie traditional morphological studies that have been used for a couple hundred years or so), and do not claim - as you seem to - that DNA is necessary to accomplish this.

What we do know is that DNA can be used to form trees of descent by the patterns of parentage left behind in descendants, and that this agrees to a very high degree with the traditional trees of descent based on the morphological patterns of parentage left behind in fossils and descendants.

This agreement is, amusingly, independent of arbitrary species designations, but entirely consistent with cladograms based on DNA and cladograms based on morphology, and the patterns of descent from common ancestors in both those cladograms being the same.

Enjoy


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RAZD
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From: the other end of the sidewalk
Joined: 03-14-2004
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Message 217 of 450 (574588)
08-16-2010 7:31 PM
Reply to: Message 210 by Big_Al35
08-16-2010 8:00 AM


Going OFF TOPIC again ...
Hi BIg_Al35,

Can I suggest you start a new thread on what DNA can and cannot tell us about evolution etc etc etc.

It seems you have an axe to grind and it really has nothing to do with the definition of species.

I think you mean to say that scientists realize that DNA offers far more answers and solutions than are currently on offer using the alternative methods.

No, what I mean is that DNA is useful for living, or recently living, organisms, for a number of things, but mostly for determining hereditary lineages.

Where we do not have DNA evidence, we do have other evidence of hereditary traits that can be used to determing hereditary lineages.

We can also test these methods against each other and see that they produce similar results.

In any event, we see that speciation is determined two ways:

(1) by evidence of the division of a breeding population into two or more daughter populations that do not interbreed, and

(b) by evidence that the breeding population has changed over time to the point where an arbitrary decision is made to call the population by a new species name.

A definition of species is useful for the latter, but it is not necessary.

Enjoy.


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RAZD
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Message 449 of 450 (653468)
02-21-2012 12:56 PM


Summation: the topic is Definition of Species
Anything not related directly to the definition of species is off-topic and should be taken to another thread to pursue, and should NOT be summarized here.

It appears that the last time the topic was addressed was ~Message 203, posted 08-06-2010.

SUMMARY

The only hard and fast definition point for species is when you have a speciation event and can observe that two or more populations evolved from a single parent population and no longer interbreed. Even so this "point" is spread out over several generations.

This definition point does not exist for asexual species or for species evolving in a lineage, when offspring become different enough from ancestors that a point is reached where one might consider them as a new species. This is necessarily rather arbitrary and somewhat subjective, unless a metric can be developed to quantify the amount of differences to use.

From Message 1

quote:
I think everyone is fairly familiar with the biological species definition, and some may be familiar with the morphological definition. Here is a site for reference on these definitions:

U of Michigan Lectures - The Process of Speciation

quote:
  • Biological species concept: This concept states that "a species is a group of actually or potentially interbreeding individuals who are reproductively isolated from other such groups."

  • Morphological species concept: Oak trees look like oak trees, tigers look like tigers. Morphology refers to the form and structure of an organism or any of its parts. The morphological species concept supports the widely held view that "members of a species are individuals that look similar to one another." This school of thought was the basis for Linneaus' original classification, which is still broadly accepted and applicable today.
  • Where we can study living populations of sexual species we can use the first definition, but when we deal with the fossil record or with asexual species we would have to use the second definition.

    There is also another definition in the forum glossary:

    http:///WebPages/Glossary.html#S

    quote:
    A basic taxonomic category for which there are various definitions. Among these are an interbreeding or potentially interbreeding group of populations reproductively isolated from other groups (the biological species concept) and a lineage evolving separately from others with its own unitary evolutionary role and tendencies (Simpson's evolutionary species concept). Employing the terms of population genetics, some definitions can be combined into the concept that a species is a population of individuals bearing distinctive genes and gene frequencies, separated from other species by biological barriers preventing gene exchange.

    These are basic common definitions of species.

    There are problems with defining exactly what species is in a way that can be applied to all living organisms. The main problem is that all species evolve, so at some point an arbitrary decision is made to call the evolved descendants a different species even though they are members of a continuum.

    This problem does not exist when speciation events are observed: we have two or more daughter populations that no longer interbreed, where both are descended from a parent population. This branching results in two closely similar pools of genes, and thus we can use the difference between those pools as a metric for comparison to arbitrary species designations:

    quote:
    Speciation is is the dividing line between what are considered microevolutionary and macroevolutionary processes and mechanisms, between the generation of homogeneous change within a population (evolution), and the generation of heterogeneous change (diversification) between diverging (especially for new) species.

    Thus I would define any population with a single peak frequency distribution as a species, any population with two peaks and a high "saddle" between them as incipient species, and any population with two peaks and a low "saddle" as different species. Analysis of this type of pattern for species like horses, zebras and donkeys would give you an idea of the saddle height necessary for speciation.


    Measuring the frequency distribution of hereditary traits within populations, and comparing them to later generations with different frequency distributions to determine when the amount of difference compares to speciation event differences would take some of the arbitrariness out of linear species assignments.

    Another possibility is to run a cladistics analysis to determine when the branching is more than seen within species between varieties.

    Enjoy.

    Edited by RAZD, : added


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