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Author Topic:   Definition of Species
fearandloathing
Member (Idle past 2312 days)
Posts: 990
From: Burlington, NC, USA
Joined: 02-24-2011


Message 226 of 450 (614084)
05-01-2011 3:04 PM
Reply to: Message 225 by Big_Al35
05-01-2011 2:52 PM


Re: Pushing back the boundaries of ignorance.
Was it on Dr. Who....it was wasn't it


"I hate to advocate the use of drugs, alcohol, violence, or insanity to anyone, but they always worked for me." - Hunter S. Thompson

Ad astra per aspera


This message is a reply to:
 Message 225 by Big_Al35, posted 05-01-2011 2:52 PM Big_Al35 has responded

Replies to this message:
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Big_Al35
Member
Posts: 384
Joined: 06-02-2010


Message 227 of 450 (614085)
05-01-2011 3:22 PM
Reply to: Message 226 by fearandloathing
05-01-2011 3:04 PM


Re: Pushing back the boundaries of ignorance.
Was it on Dr. Who....it was wasn't it

What are the options? Eastenders, Dr Who, Top Gear....to name but three.


This message is a reply to:
 Message 226 by fearandloathing, posted 05-01-2011 3:04 PM fearandloathing has not yet responded

Replies to this message:
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 Message 229 by Wounded King, posted 05-01-2011 5:55 PM Big_Al35 has responded

    
Admin
Director
Posts: 12602
From: EvC Forum
Joined: 06-14-2002
Member Rating: 3.7


Message 228 of 450 (614086)
05-01-2011 4:19 PM
Reply to: Message 227 by Big_Al35
05-01-2011 3:22 PM


Topic Reminder
Unless you can show how what you learned from the program relates to the topic of this thread about the definition of species, I think you're off-topic. I was letting it go under the assumption that it would be a short diversion from the topic, but you seem to want to play 20 questions.

Please feel free to propose a new topic to discuss this over at Proposed New Topics.


--Percy
EvC Forum Director

This message is a reply to:
 Message 227 by Big_Al35, posted 05-01-2011 3:22 PM Big_Al35 has not yet responded

    
Wounded King
Member (Idle past 2261 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 229 of 450 (614091)
05-01-2011 5:55 PM
Reply to: Message 227 by Big_Al35
05-01-2011 3:22 PM


Could you be more specific?
I assume the program you were watching was the gene code, but unless you are more specific in where the claim you are discussing is made, and since it is on I-player you could have told us the program and even told us the right time point had you cared about productive discussion, it is hard to address what claim it is you are talking about.

A brief skim view suggests that perhaps what you are misunderstanding is the concept of conservation, where some regions of DNA appear to have undergone substantial random mutation while others seem to have been very precisely maintained across vastly distinct species, i.e. chickens and humans.

Your mistake is in believing that this is somehow controlled by the DNA. What it is is the result of natural selection removing mutations which are deleterious. If a specific nucleotide sequence is vital to the development, survival or reproductive success of the organism then it will tend to be highly conserved.

This doesn't mean that there is anything preventing mutations happening in these regions, it just means that when they do the organisms in which they arise do not tend to contribute their genes to future generations.

You could argue I suppose that since the organism's genome is part of its whole environment then through the complex interconnected nature of the gene regulatory networks the rest of the genome is one of the selective factors which constrains which mutations are viable. But if that was what you were trying to say you said it very badly, and it is totally irrelevant to defining species.

So if you want to discuss specifics then give us some specific to discuss, either in your own words or by giving us a time code for when in the program the comments you are interested in are.

TTFN,

WK

Edited by Wounded King, : No reason given.


This message is a reply to:
 Message 227 by Big_Al35, posted 05-01-2011 3:22 PM Big_Al35 has responded

Replies to this message:
 Message 230 by Big_Al35, posted 05-02-2011 6:49 AM Wounded King has responded

    
Big_Al35
Member
Posts: 384
Joined: 06-02-2010


Message 230 of 450 (614121)
05-02-2011 6:49 AM
Reply to: Message 229 by Wounded King
05-01-2011 5:55 PM


Re: Could you be more specific?
Wounded King writes:

What it is is the result of natural selection removing mutations which are deleterious. If a specific nucleotide sequence is vital to the development, survival or reproductive success of the organism then it will tend to be highly conserved.

Both you and Huntard have already given examples of three legged individuals which I would describe as highly deleterious. You didn't make the distinction before between highly conserved sequences within the genome and those which are not highly conserved. The sequence of DNA which specifies having two legs falls within those precisely defined and highly maintained segments of DNA that we are talking about.

I believe that you and your side kick Huntard are therefore to blame for this going off-topic. You presented your arguments as if there was no distinction between highly mutated areas and those that are more precisely maintained. Ofcourse you're back peddaling now.

I don't dispute that any area of the genome is vulnerable to being perturbed, but clearly we both agree that some areas are highly maintained whereas within other seqments of DNA code, non-deleterious mutations occur often, frequently and infact with every offspring.


This message is a reply to:
 Message 229 by Wounded King, posted 05-01-2011 5:55 PM Wounded King has responded

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 Message 232 by Wounded King, posted 05-02-2011 9:02 AM Big_Al35 has responded

    
Admin
Director
Posts: 12602
From: EvC Forum
Joined: 06-14-2002
Member Rating: 3.7


Message 231 of 450 (614125)
05-02-2011 7:46 AM
Reply to: Message 230 by Big_Al35
05-02-2011 6:49 AM


Re: Could you be more specific?
Hi Big_Al35,

If you have a topic you would like to discuss that isn't related to the definition of species then please propose it over at Proposed New Topics.


--Percy
EvC Forum Director

This message is a reply to:
 Message 230 by Big_Al35, posted 05-02-2011 6:49 AM Big_Al35 has not yet responded

    
Wounded King
Member (Idle past 2261 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 232 of 450 (614128)
05-02-2011 9:02 AM
Reply to: Message 230 by Big_Al35
05-02-2011 6:49 AM


Re: Could you be more specific?
Just a quick aside to Percy:

This is actually veering back round to the original topic as what we were discussing previously was the distinction between morphospecies and genetic distance based species definitions. Specifically many of us were trying to make Big_Al understand both the arbitrary nature of species definitions and the disconnect between morphology and DNA which meant that morphologically identical species could be significantly divergent in their genomes. This then took us on to discussing morphological variability which was not genetically determined, something Big_Al appeared not to believe in.

Big_Al35 writes:

Both you and Huntard have already given examples of three legged individuals which I would describe as highly deleterious.

I would certainly agree with you, and I suspect Huntard would to, but you still seem to have failed to grasp the point we were making, which is that this is not a genetic mutation.

You presented your arguments as if there was no distinction between highly mutated areas and those that are more precisely maintained. Ofcourse you're back peddaling now.

The whole reason we got onto the three legged issue was because you were denying the role of environmental factors in affecting development. That is why were weren't discussing conserved or non-conserved regions of the genome, because the whole point was that there are extra-genomic factors that can affect an embryo's development.

The sequence of DNA which specifies having two legs falls within those precisely defined and highly maintained segments of DNA that we are talking about.

I think the idea that there is one 'sequence of DNA which specifies having two legs' is probably quite mistaken. I am quite happy to accept that there is probably a high degree of conservation amongst the various genes and regulatory elements which produce bilaterally symmetric limbs amongst vertebrates.

I don't dispute that any area of the genome is vulnerable to being perturbed, but clearly we both agree that some areas are highly maintained whereas within other seqments of DNA code, non-deleterious mutations occur often, frequently and infact with every offspring.

I think you are making a false distinction here, the important thing is not the frequency and nature of the mutation but it's subsequent spread through the population.

There is little reason to think that highly conserved regions are any less susceptible to mutation than non-conserved regions, conservation is principally a reflection of natural selection rather than mutational frequencies. The important distinction is not that the mutations occur in these non-conserved regions but that they are allowed to persist in them while similar mutations in more developmentally/functionally important regions will tend to be selected against because of the perturbations they produce. In the most extreme cases this selection will be virtually immediate in the form of embryonic lethal mutations where the organism will never become viable.

TTFN,

WK


This message is a reply to:
 Message 230 by Big_Al35, posted 05-02-2011 6:49 AM Big_Al35 has responded

Replies to this message:
 Message 233 by Admin, posted 05-02-2011 12:57 PM Wounded King has not yet responded
 Message 234 by Big_Al35, posted 05-03-2011 3:41 PM Wounded King has responded

    
Admin
Director
Posts: 12602
From: EvC Forum
Joined: 06-14-2002
Member Rating: 3.7


Message 233 of 450 (614165)
05-02-2011 12:57 PM
Reply to: Message 232 by Wounded King
05-02-2011 9:02 AM


Re: Could you be more specific?
Wounded King writes:

Just a quick aside to Percy:

This is actually veering back round to the original topic as what we were discussing previously was the distinction between morphospecies and genetic distance based species definitions. Specifically many of us were trying to make Big_Al understand both the arbitrary nature of species definitions and the disconnect between morphology and DNA which meant that morphologically identical species could be significantly divergent in their genomes. This then took us on to discussing morphological variability which was not genetically determined, something Big_Al appeared not to believe in.

Thanks for explaining how this relates to the topic. Carry on, everyone.


--Percy
EvC Forum Director

This message is a reply to:
 Message 232 by Wounded King, posted 05-02-2011 9:02 AM Wounded King has not yet responded

    
Big_Al35
Member
Posts: 384
Joined: 06-02-2010


Message 234 of 450 (614331)
05-03-2011 3:41 PM
Reply to: Message 232 by Wounded King
05-02-2011 9:02 AM


Re: Could you be more specific?
The whole reason we got onto the three legged issue was because you were denying the role of environmental factors in affecting development. That is why were weren't discussing conserved or non-conserved regions of the genome, because the whole point was that there are extra-genomic factors that can affect an embryo's development.

If I agreed or disagreed about the influence that the environment has on a developing embryo the issue for evolution remains the same. Evolutionary theory works on the principal that we are all related as we all share common DNA. If the example you gave was of the impact of an extra-genomic factor unrelated to genetic mutation then your point is irrelevant to the study of evolution.

I think you are making a false distinction here, the important thing is not the frequency and nature of the mutation but it's subsequent spread through the population.

I think your reasoning here is a non sense. Highly conserved genes have spread throughout the population and therefore would be the genes that identify species more accurately. Those sequences which appear in the randomized segments of the DNA code can in many instances morph in the following offspring. This does not a species make.

There is little reason to think that highly conserved regions are any less susceptible to mutation than non-conserved regions

A highly conserved region is by definition less susceptible to mutation than non-conserved regions.

mutations in more developmentally/functionally important regions will tend to be selected against because of the perturbations they produce. In the most extreme cases this selection will be virtually immediate in the form of embryonic lethal mutations where the organism will never become viable.

If mutation in more important regions tend to be selected against due to the potential of non viable organisms this adds weight to the argument that it should be these sequences of DNA that should be used to identify species and not the more mutated areas.


This message is a reply to:
 Message 232 by Wounded King, posted 05-02-2011 9:02 AM Wounded King has responded

Replies to this message:
 Message 235 by Wounded King, posted 05-03-2011 4:40 PM Big_Al35 has responded

    
Wounded King
Member (Idle past 2261 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 235 of 450 (614340)
05-03-2011 4:40 PM
Reply to: Message 234 by Big_Al35
05-03-2011 3:41 PM


Highly conserved sequences
If the example you gave was of the impact of an extra-genomic factor unrelated to genetic mutation then your point is irrelevant to the study of evolution.

That was my point, you were the one saying that there weren't organisms being born with extra legs because the environment couldn't affect DNA and claiming that the variations in fingerprints and retina must be encoded in DNA.

I was pointing out that extra-genomic environmental factors were a strong influence on the random/stochastic elements of development which produce a further level of variation beyond that encoded in the DNA.

But since this variation is not heritable it is not relevant to evolution, whereas in your scenario where all the variation is somehow coded into the DNA it would be.

Highly conserved genes have spread throughout the population and therefore would be the genes that identify species more accurately.

No. In fact genes that aren't at all conserved across species would be best to uniquely identify a species. What conserved genes are good for is to produce phylogenies across multiple species. There can be conservation of a gene within a species but not between species such a species specific gene would be the ideal molecular marker.

A highly conserved region is by definition less susceptible to mutation than non-conserved regions.

No it isn't, it is just that the organisms in which it is mutated are much less likely to survive and reproduce. There is no protective effect stopping mutations form occurring it is post hoc natural selection that is eliminating the mutants.

More reasonably by definition a conserved region is one in which significant divergent mutations have not accumulated, that doesn't mean that those mutations can't occur.

If you think you can find a reputable source to support your definition feel free to provide it.

TTFN,

WK


This message is a reply to:
 Message 234 by Big_Al35, posted 05-03-2011 3:41 PM Big_Al35 has responded

Replies to this message:
 Message 236 by Big_Al35, posted 05-03-2011 5:16 PM Wounded King has responded

    
Big_Al35
Member
Posts: 384
Joined: 06-02-2010


Message 236 of 450 (614344)
05-03-2011 5:16 PM
Reply to: Message 235 by Wounded King
05-03-2011 4:40 PM


Re: Highly conserved sequences
No. In fact genes that aren't at all conserved across species would be best to uniquely identify a species

You are talking about genes conserved or not conserved across species, whereas I am talking about genes conserved or not conserved through the generations of one species. Note that DNA is very effective in determining paternity and kinship.

No it isn't, it is just that the organisms in which it is mutated are much less likely to survive and reproduce

This is not my understanding of how DNA works. My parents had several children each one with different DNA however small. They did not have several miscarriages to balance out the successful outcomes which would be the logical conclusion of your argument.

If you think you can find a reputable source to support your definition feel free to provide it.

You didn't need much information to identify the program I was referring to and the same follows for the above.


This message is a reply to:
 Message 235 by Wounded King, posted 05-03-2011 4:40 PM Wounded King has responded

Replies to this message:
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 Message 238 by Percy, posted 05-03-2011 7:15 PM Big_Al35 has responded

    
Wounded King
Member (Idle past 2261 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 237 of 450 (614347)
05-03-2011 5:58 PM
Reply to: Message 236 by Big_Al35
05-03-2011 5:16 PM


Re: Highly conserved sequences
This is not my understanding of how DNA works. My parents had several children each one with different DNA however small. They did not have several miscarriages to balance out the successful outcomes which would be the logical conclusion of your argument.

Well I think we have fairly well established that you don't have a particularly solid grasp of how DNA works. Your argument fails to make sense though, what basis are you using to claim that logically your parents should have suffered several miscarriages? Can you show me appropriate mutation rates and the exact number of 100% obligatory nucleotide sequences that support your claim? If so then you know more about human genetics than anyone else on the planet.

As I pointed out embryonic lethals are the most extreme form of the operation of selection that I described. But it is worth noting that your parents may have had a miscarriage and been unaware of it, there is evidence that as many as 25% of natural conceptions end in miscarriage within the first 6 weeks of pregnancy (Wilcox et al., 1999). It is also worthwhile noting that anyone who is congenitally sterile would satisfy the most extreme criteria as well.

This doesn't begin to take into account non-lethal, non-sterility causing mutations which nevertheless significantly impact survival and reproductive success leading to a tendency not to propagate.

You didn't need much information to identify the program I was referring to and the same follows for the above.

No I didn't, but the program doesn't use your definition at all. They are talking about the conservation of sequences between chickens and humans. And since I know that your definition is nonsense, since I have studied and worked in the field of genetics for 15 years, I am hardly going to waste my time looking for a reputable source that uses it.

So since you are claiming that is the definition why is it you can't you tell me where you saw it defined that way?

TTFN,

WK


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Percy
Member
Posts: 18484
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.8


Message 238 of 450 (614362)
05-03-2011 7:15 PM
Reply to: Message 236 by Big_Al35
05-03-2011 5:16 PM


Re: Highly conserved sequences
Big_Al35 writes:

You are talking about genes conserved or not conserved across species, whereas I am talking about genes conserved or not conserved through the generations of one species.

I think you can safely assume that to a very great extent genes are conserved through the generations of a species. The genes of a species practically define it. Maybe it is alleles you are thinking of?

There are some examples from the plant world of some lines of a species not sharing all the same genes, but this is so unexpected as to be worthy of note in the technical literature, e.g.:

http://www.sciencedaily.com/...ases/2010/11/101123121117.htm

While you're not wrong in believing that it is not always the case that genes are conserved within the same species, it is by far the exception and doesn't apply to any worthy extent to the example of human reproduction you're discussing with WK.

--Percy


This message is a reply to:
 Message 236 by Big_Al35, posted 05-03-2011 5:16 PM Big_Al35 has responded

Replies to this message:
 Message 239 by Big_Al35, posted 05-04-2011 3:47 AM Percy has responded

    
Big_Al35
Member
Posts: 384
Joined: 06-02-2010


Message 239 of 450 (614402)
05-04-2011 3:47 AM
Reply to: Message 238 by Percy
05-03-2011 7:15 PM


Re: Highly conserved sequences
Wounded King writes:

Well I think we have fairly well established that you don't have a particularly solid grasp of how DNA works.

Firstly you gave me an example of a three legged individual whose deformity was due to environmental impact and therefore irrelevant to the study of genetics or evolution and you claim that I don't have a solid grasp?

It would appear that you don't have a solid grasp of reality or the relevant.

Wounded King writes:

They are talking about the conservation of sequences between chickens and humans

You will persist in this game of making utterly irrelevant points in your show of brinksmanship. Who cares about the conservation of sequences between chickens and humans? I could point out that 85% of the genome between mice and humans is the same too. It's utterly irrelevant again. Humans, mice and chickens are all different species which didn't even evolve along the same paths if they evolved at all. It's not about which sequences are the same but about which sequences are different.

Percy writes:

The genes of a species practically define it.

This is a tautology and poor logic. Something that evolutionists seem to thrive on. That's why we are here discussing the title of this forum.

Percy writes:

I think you can safely assume that to a very great extent genes are conserved through the generations of a species

Are you disputing Darwinian natural selection? Sounds like it to me.


This message is a reply to:
 Message 238 by Percy, posted 05-03-2011 7:15 PM Percy has responded

Replies to this message:
 Message 240 by Wounded King, posted 05-04-2011 4:53 AM Big_Al35 has responded
 Message 241 by Percy, posted 05-04-2011 8:17 AM Big_Al35 has not yet responded

    
Wounded King
Member (Idle past 2261 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 240 of 450 (614408)
05-04-2011 4:53 AM
Reply to: Message 239 by Big_Al35
05-04-2011 3:47 AM


Re: Highly conserved sequences
Firstly you gave me an example of a three legged individual whose deformity was due to environmental impact and therefore irrelevant to the study of genetics or evolution and you claim that I don't have a solid grasp?

It would appear that you don't have a solid grasp of reality or the relevant.

Okay, so apparently you have completely forgotten the previous discussion on this thread. Why not look at Message 204 where you say that the random factors affecting fingerprint and retina patterns must be encoded in the genome and take up considerable space there, or look at Message 212, where you ask ...

How can the variable nature of the environment affect some parts of the DNA but not the important information storing parts which spell out that we should have arms, legs, torso, head etc...I am guessing you are going to tell me now that some people are born with three legs?

What I was doing is pointing out to you what is really the case with these sort of variations, that the randomisation comes from the environment and also in part from the statistical mechanical nature of biochemistry. These random factors aren't affecting the DNA but rather the functional activities that the genes encode for during development and in some cases the expression level and timing of particular genes.

So your whole swathe of genetic information acting as a random seed for variation is a complete fabrication you made up of whole cloth, and now we are supposed to accept that you know what you are talking about? Especially hard to do when you claim I am dragging things off topic when I answer specific questions that you have asked.

You will persist in this game of making utterly irrelevant points in your show of brinksmanship. Who cares about the conservation of sequences between chickens and humans?

The people in the TV program you were claiming supported your claim that ...

DNA is coded such that it specifies which sequences of DNA code can change randomly and which areas should not be changed randomly

You have yet to identify a point in the program which actually supports this claim. I identified what I thought might be the relevant segment where they talk about highly conserved regions across species, if this wasn't what you meant then why not, actually finally after half a dozen posts, give us a useful point of reference so we know exactly what you are talking about, or even give us the relevant quotes since all you need to do is transcribe them from i-player.

It's utterly irrelevant again. Humans, mice and chickens are all different species which didn't even evolve along the same paths if they evolved at all.

Well if one accepts evolution then they did evolve along exactly the same paths up until they diverged from their respective most recent common ancestors.

It's not about which sequences are the same but about which sequences are different.

Wasn't that kind of my point? That between species differences rather than commonalities were more appropriate for defining species?

I get the impression that the segment I identified wasn't actually the one you were thinking of, if this is the case it would have been a lot less confusing if you had just said so at once and identified the correct segment.

If you want to set an arbitrary limit on the genetic distance from a given genotype or an arbitrary set of molecular markers or haplotypes that defines a species (as in species barcodes) then I am quite happy with that, as long as you appreciate that it is arbitrary.

If you are claiming that your criteria aren't arbitrary then you need to provide some sort of rationale for why not. I understand the basis for your claim that there should be some clear demarcation, some form of created kinds argument or baraminology, but that isn't a rationale for choosing any particular set of criteria.

TTFN,

WK


This message is a reply to:
 Message 239 by Big_Al35, posted 05-04-2011 3:47 AM Big_Al35 has responded

Replies to this message:
 Message 242 by Big_Al35, posted 05-04-2011 9:19 AM Wounded King has responded

    
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