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Author Topic:   Definition of Species
Percy
Member
Posts: 18364
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.8


Message 241 of 450 (614418)
05-04-2011 8:17 AM
Reply to: Message 239 by Big_Al35
05-04-2011 3:47 AM


Re: Highly conserved sequences
Big_Al35 writes:

Percy writes:

The genes of a species practically define it.

This is a tautology and poor logic.

I think you're confusing tautologies with definitions. Take this, for example:

  • The winner is the fastest in a race.
  • The fastest in a race is the winner.

By your logic this is a tautology, as would be all definitions. When you tell us your definition of a species, by your logic it will be a tautology. I think you need to look up tautology.

That the genes of a species are representative is why we can discover through DNA analysis that what were believed a single species of elephant is actually two (e.g., Africa Has Two Elephant Species, Genetic Analysis Confirms).

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.

But as we've discovered in this thread, what things "sound like to you" often has little to do with their actual meaning.

The genes of a species are highly conserved. That's why DNA from the 5300 year-old iceman discovered in the Alps has all the same genes modern humans have. From this we know he was human, like us.

But reproduction is not perfect (mutation), both random and natural selection filter gene alleles, and over time, particularly under changing environmental circumstances, the genes that make up a species can evolve to form a new species. And we can verify that it's a new species by comparing genes through DNA analysis, because the genes that make up a species are uniquely representative.

One can legitimately ask how a static definition of species as being defined by its genes fits into a dynamic evolutionary context where genes can change and appear and disappear over time.

One can also legitimately ask how one determines species during a transitional period. You've probably heard it said that all species are transitional, but the change is very slow. Over relatively short periods like 10,000 years it is much more true than not that genes are conserved within a species.

--Percy


This message is a reply to:
 Message 239 by Big_Al35, posted 05-04-2011 3:47 AM Big_Al35 has not yet responded

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


Message 242 of 450 (614424)
05-04-2011 9:19 AM
Reply to: Message 240 by Wounded King
05-04-2011 4:53 AM


Re: Highly conserved sequences
Wounded King writes:

randomisation comes from the environment

Ok I accept that fingerprints and retinas have an environmental influence. This doesn't change the fact that you will persist on highlighting irrelevancies again and again. Fingerprints and retinas do not define species and environmental influences do not define species.

Wounded King writes:

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

You have a remarkable capacity to highlight the irrelevant, confuse the issue, and make ad hoc comparisons. As I said before who cares about human and chicken similarities. Why a chicken and not an elephant? Commonalities between humans and random creatures is just a diversion from the real issue which you continue to avoid.

You continually refer to conserved areas across species but never refer to conserved areas within one species. I am guessing it's due to Percys subsequent contributions which are just plain flawed.

As I stated before it makes more sense to study one species and highlight the divergences and commonalities there as your starting point.

Percy writes:

I think you're confusing tautologies with definitions.

Percy writes:

The genes of a species practically define it.

Firstly, why are we discussing the definition of species when you, apparently, have it all figured out in your above wisdom. If this was and is the case I think we can close this thread right now.

Secondly, it's still a tautology as you are adding no additional knowledge here. I know it must be hard for you to part with any wisdom or to share in your experience but it would be helpful if you tried.


This message is a reply to:
 Message 240 by Wounded King, posted 05-04-2011 4:53 AM Wounded King has responded

Replies to this message:
 Message 243 by Percy, posted 05-04-2011 9:28 AM Big_Al35 has not yet responded
 Message 244 by Wounded King, posted 05-04-2011 10:07 AM Big_Al35 has responded

    
Percy
Member
Posts: 18364
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.8


Message 243 of 450 (614425)
05-04-2011 9:28 AM
Reply to: Message 242 by Big_Al35
05-04-2011 9:19 AM


Re: Highly conserved sequences
Big_Al35 writes:

Firstly, why are we discussing the definition of species when you, apparently, have it all figured out in your above wisdom. If this was and is the case I think we can close this thread right now.

Secondly, it's still a tautology as you are adding no additional knowledge here. I know it must be hard for you to part with any wisdom or to share in your experience but it would be helpful if you tried.

I'm not sure I understand your problem, Al. I stated my position and provided supporting evidence. A shared set of genes is how we identify species, and I provided two examples and additional paragraphs of information. There was the example of sifting through genes to tell that what was thought a single species of elephant was actually two, and there was the 5300 year-old iceman who shares all our genes. I described how reproduction is imperfect and that genes will change and appear and disappear over time, but that on shorter time scales genes of species are generally conserved. There was a lot there - maybe you could respond to it instead of taking all of 10 seconds to make inaccurate complaints.

--Percy

Edited by Percy, : Grammar.

Edited by Percy, : Grammar.


This message is a reply to:
 Message 242 by Big_Al35, posted 05-04-2011 9:19 AM Big_Al35 has not yet responded

    
Wounded King
Member (Idle past 2198 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


(1)
Message 244 of 450 (614427)
05-04-2011 10:07 AM
Reply to: Message 242 by Big_Al35
05-04-2011 9:19 AM


CAOS theory
I'll be honest Big_Al, I'm having a hard time seeing this as you trying to engage in a productive debate.

This doesn't change the fact that you will persist on highlighting irrelevancies again and again. Fingerprints and retinas do not define species and environmental influences do not define species.

Irrelevancies that you brought into the discussion and accompanied with a gigantic false claim concerning genetics.

As I said before who cares about human and chicken similarities.

Lots of people who study comparative genetics do, including some from the documentary you directed us all to.

Why a chicken and not an elephant?

Because chickens are easily experimentally manipulable and readily produced in great numbers, none of which are true for elephants. Also chickens are considerably further removed from us in evolutionary distance, meaning that conservations across that distance are more likely to be functionally important.

You continually refer to conserved areas across species but never refer to conserved areas within one species.

We don't really have enough human genomes sequenced yet to be able to say too much about this. Things like the HapMap project and the 1000 genomes project are good starts though.

I think you are wrong to ignore cross species comparisons though, there is no point defining a suite of genetic characteristics common to all humans as a species definition if you then find out that the same characteristic suite is found in chimps and gorillas as well. You need both to come up with a suitable criteria.

Since you brought up DNA barcoding earlier on a suitable paper for discussion might be this one ...

Rach et al., 2008 writes:

Character-based DNA barcoding allows discrimination of genera, species and populations in Odonata

Proc Biol Sci. 2008 February 7; 275(1632): 237–247.

DNA barcoding has become a promising means for identifying organisms of all life stages. Currently, phenetic approaches and tree-building methods have been used to define species boundaries and discover ‘cryptic species’. However, a universal threshold of genetic distance values to distinguish taxonomic groups cannot be determined. As an alternative, DNA barcoding approaches can be ‘character based’, whereby species are identified through the presence or absence of discrete nucleotide substitutions (character states) within a DNA sequence. We demonstrate the potential of character-based DNA barcodes by analysing 833 odonate specimens from 103 localities belonging to 64 species. A total of 54 species and 22 genera could be discriminated reliably through unique combinations of character states within only one mitochondrial gene region (NADH dehydrogenase 1). Character-based DNA barcodes were further successfully established at a population level discriminating seven population-specific entities out of a total of 19 populations belonging to three species. Thus, for the first time, DNA barcodes have been found to identify entities below the species level that may constitute separate conservation units or even species units. Our findings suggest that character-based DNA barcoding can be a rapid and reliable means for (i) the assignment of unknown specimens to a taxonomic group, (ii) the exploration of diagnosability of conservation units, and (iii) complementing taxonomic identification systems.

What you propose seems to be similar to this characteristic attribute organization system (CAOS) approach. But this approach relies on the fact that members of a given taxonomic group share attributes (e.g. polymorphisms) that are absent from comparable groups. This approach explicitly relies on both within and between group comparisons to define a meaningful suite of diagnostic characteristics.

Can you outline what sort of approach you would take to usefully define a species genetically looking only within that species?

TTFN,

WK

Edited by Wounded King, : No reason given.


This message is a reply to:
 Message 242 by Big_Al35, posted 05-04-2011 9:19 AM Big_Al35 has responded

Replies to this message:
 Message 245 by Big_Al35, posted 05-05-2011 6:21 AM Wounded King has responded

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


Message 245 of 450 (614579)
05-05-2011 6:21 AM
Reply to: Message 244 by Wounded King
05-04-2011 10:07 AM


Re: CAOS theory
Wounded King writes:

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

The above statement is completely illogical. Let me explain why.

Consider three species, humans, mice and chickens.

Lets say that one individual human has the following genome; ABCDEFGHIJK
Lets say that one individual mouse has ; ABCDEFLMNOP
And one individual chicken has; ABCDPQRST

If we do what you are suggesting and use the differences to define species we get the following result;

human - chicken differences are ; EFGHIJK - PQRST
human - mice differences are ; GHIJK - LMNOP
chicken - mice differences are ; QRST - EFLMNO

You can see how unhelpful the results are and no definition can be reached.

If we consider the commonalities we get ;

human - chicken commonalities are ; ABCD
human - mice commonalities are ; ABCDEF
chicken - mice commonalities are ; ABCDP

Again not helpful.

Now consider two humans, the one above has genome ABCDEFGHIJK and another with ABCDEFGHIVW

The differences are JK - VW and the commonalities are
ABCDEFGHI. If we were to find a third, fourth and fifth human with a matching genome of ABCDEFGHI we might start to think that ABCDEFGHI could be used as a good and reliable definition for a human.


This message is a reply to:
 Message 244 by Wounded King, posted 05-04-2011 10:07 AM Wounded King has responded

Replies to this message:
 Message 246 by Wounded King, posted 05-05-2011 6:49 AM Big_Al35 has responded
 Message 249 by Percy, posted 05-05-2011 9:21 AM Big_Al35 has responded

    
Wounded King
Member (Idle past 2198 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 246 of 450 (614581)
05-05-2011 6:49 AM
Reply to: Message 245 by Big_Al35
05-05-2011 6:21 AM


Re: CAOS theory
You can see how unhelpful the results are and no definition can be reached.

Incorrect, it is worth noting that between species differences are not simply studied on the basis of 1 individual organism. But putting that aside we clearly already have a panel of putative diagnostic characters that could define the 3 species.

Chicken: QRST
Mouse: LMNO
Human: GHIJK

Obviously the accuracy of these can be refined both by the study of other species and of further individuals within each species. This is much more useful for defining a species than the commonalities from the cross species analysis, as I said it would be.

If we were to find a third, fourth and fifth human with a matching genome of ABCDEFGHI we might start to think that ABCDEFGHI could be used as a good and reliable definition for a human.

And when we find a chimpanzee with ABCDEFGHIST? That is the limitation of your only within approach. In fact no matter how many humans you find with ABCDEFGHI it will never be a suitable definition if you haven't looked at other, ideally closely related, species because you simply won't know what their characteristics, and consequently any characteristics shared with humans, are.

This is why I have been saying all along that you need to look at both within and between species variation.

TTFN,

WK


This message is a reply to:
 Message 245 by Big_Al35, posted 05-05-2011 6:21 AM Big_Al35 has responded

Replies to this message:
 Message 247 by Big_Al35, posted 05-05-2011 8:08 AM Wounded King has responded

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


Message 247 of 450 (614586)
05-05-2011 8:08 AM
Reply to: Message 246 by Wounded King
05-05-2011 6:49 AM


Re: CAOS theory
Wounded King writes:

we clearly already have a panel of putative diagnostic characters that could define the 3 species.

Human: GHIJK

Incorrect, as my example already goes on to find a human with
GHIVW.

This is why I have been saying all along that you need to look at both within and between species variation.

Yes you have kept referring to conservation across the species but never conservation within one species see previous posts.


This message is a reply to:
 Message 246 by Wounded King, posted 05-05-2011 6:49 AM Wounded King has responded

Replies to this message:
 Message 248 by Wounded King, posted 05-05-2011 9:00 AM Big_Al35 has not yet responded

    
Wounded King
Member (Idle past 2198 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 248 of 450 (614587)
05-05-2011 9:00 AM
Reply to: Message 247 by Big_Al35
05-05-2011 8:08 AM


Re: CAOS theory
Al writes:

Incorrect, as my example already goes on to find a human with GHIVW.

Fine, my whole point was that from comparisons of the initial 3 individual organisms you had a preliminary basis to be further refined. So you add another couple of humans in and find that only GHI are species specific, and maybe you find that JK is population specific to Kalahari bushmen, whatever.

Al writes:

Yes you have kept referring to conservation across the species but never conservation within one species see previous posts.

I have also referred to conservation within species, see previous posts. Again, since you seem to be incredibly resistant to reading what I actually write, what is needed to produce a useful definition is both within and between species comparisons. In fact the most important things to look at for defining a species are differences between species and similarities within species, which was why I said exactly that in Message 235.

WK writes:

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.

This whole recurrence of the thread just seems another prime example of you bringing up something irrelevant, the as yet unidentified claim made in the BBC program which you say supports ...

Al writes:

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

And then when people address this you act as if you were talking about the original topic all along and claim that other people are talking about irrelevancies, i.e. the cross species conservation which was discussed in the BBC program.

If the cross species conservation wasn't what you were talking about then why not finally pull your finger out and identify what it was in the program that you were talking about, it has been several days now and you have still to do the most basic thing to actually provide any support for your claim, or even show how you relate that claim to the central topic.

I have tried to steer the topic back to a more focused discussion of species and cited a paper using a genetic barcoding approach which emphasises the importance of both within and between species/population comparisons. Do you agree yet that a within species only approach is insufficient?

TTFN,

WK


This message is a reply to:
 Message 247 by Big_Al35, posted 05-05-2011 8:08 AM Big_Al35 has not yet responded

    
Percy
Member
Posts: 18364
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.8


Message 249 of 450 (614589)
05-05-2011 9:21 AM
Reply to: Message 245 by Big_Al35
05-05-2011 6:21 AM


Re: CAOS theory
Big_Al35 writes:

Now consider two humans, the one above has genome ABCDEFGHIJK and another with ABCDEFGHIVW.

Each letter corresponds to a gene, right? I believe it would be very uncommon to find two humans who did not share the same set of genes, maybe down around the 1% level. There are many sources of genetic differences, and deletions, the only way to lose a gene in a single generation (it being extremely unlikely, though not impossible, for there to be multiple single nucleotide substitutions and/or other copying errors in the same gene occurring to the point of rendering it unrecognizable) tend to cause serious genetic diseases, or probably more likely, unviable zygotes (sperm/egg unions).

I interpret WK's posts as accepting that differences in gene subsets in the human population are common, but I didn't believe that was the case yesterday, and now after having spent a half hour with Wikipedia reading the articles on Human Genetic Variation, The Human Genome, Deletions, Insertions, etc., I feel even more confirmed in this belief.

Maybe I'm misinterpreting WK, or maybe I'm wrong, but either way clarification would be appreciated.

--Percy


This message is a reply to:
 Message 245 by Big_Al35, posted 05-05-2011 6:21 AM Big_Al35 has responded

Replies to this message:
 Message 250 by Wounded King, posted 05-05-2011 9:36 AM Percy has acknowledged this reply
 Message 251 by Big_Al35, posted 05-05-2011 10:03 AM Percy has responded

    
Wounded King
Member (Idle past 2198 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 250 of 450 (614591)
05-05-2011 9:36 AM
Reply to: Message 249 by Percy
05-05-2011 9:21 AM


Re: CAOS theory
I'd been considering these characteristics to be more akin to haplotypes or single nucleotide polymorphisms (SNPs) rather than actual discrete genes. Certainly SNPs within a gene or set of genes is the usual basis for DNA barcoding approaches.

TTFN,

WK


This message is a reply to:
 Message 249 by Percy, posted 05-05-2011 9:21 AM Percy has acknowledged this reply

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


Message 251 of 450 (614593)
05-05-2011 10:03 AM
Reply to: Message 249 by Percy
05-05-2011 9:21 AM


Percy writes:

Each letter corresponds to a gene, right?

No the genome consists of the entire DNA architecture of which genes make less than 3%. Even when comparing known genes, as you have already stated, significant differences will be noted due to the many different alleles.


This message is a reply to:
 Message 249 by Percy, posted 05-05-2011 9:21 AM Percy has responded

Replies to this message:
 Message 252 by Percy, posted 05-05-2011 10:21 AM Big_Al35 has responded

    
Percy
Member
Posts: 18364
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.8


Message 252 of 450 (614597)
05-05-2011 10:21 AM
Reply to: Message 251 by Big_Al35
05-05-2011 10:03 AM


Big_Al35 writes:

No the genome consists of the entire DNA architecture of which genes make less than 3%. Even when comparing known genes, as you have already stated, significant differences will be noted due to the many different alleles.

Ah, that makes more sense, but in that case everything I said in Message 241 about gene sets being unique to species is still accurate. And WK agrees, as he said in Message 248, "I have also referred to conservation within species," and though here I think he's referring to the SNP and haplotype levels, that means conservation is even stronger at the higher level of genes.

If I've interpreted him properly, I think that WK is now seeking to find whether you will agree that barcoding by itself is insufficient for species identification. If you can say yea or nay on this it might make it easier to move forward.

--Percy


This message is a reply to:
 Message 251 by Big_Al35, posted 05-05-2011 10:03 AM Big_Al35 has responded

Replies to this message:
 Message 253 by Big_Al35, posted 05-05-2011 10:40 AM Percy has responded
 Message 254 by Wounded King, posted 05-05-2011 10:46 AM Percy has responded

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


Message 253 of 450 (614599)
05-05-2011 10:40 AM
Reply to: Message 252 by Percy
05-05-2011 10:21 AM


Percy writes:

everything I said in Message 241 about gene sets being unique to species is still accurate. And WK agrees

Thats very interesting given that we share 98% of our entire genome with chimpanzees and yet only 2-3% of the genome consists of genes!

It would be interesting to discover how many genes are different between humans and chimps and what fraction of the entire genome this represents?


This message is a reply to:
 Message 252 by Percy, posted 05-05-2011 10:21 AM Percy has responded

Replies to this message:
 Message 256 by Wounded King, posted 05-05-2011 11:17 AM Big_Al35 has not yet responded
 Message 257 by Percy, posted 05-05-2011 9:17 PM Big_Al35 has responded

    
Wounded King
Member (Idle past 2198 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 254 of 450 (614601)
05-05-2011 10:46 AM
Reply to: Message 252 by Percy
05-05-2011 10:21 AM


I think that WK is now seeking to find whether you will agree that barcoding by itself is insufficient for species identification.

It isn't quite that, DNA barcodes are very effective for Species identification as long as you have a reference, what they aren't necessarily good for is species discovery.

If we are naively presented with a panel of genetic sequences from an unknown set of organisms then we can use the approaches used for genetic barcoding to identify specific populations. we can produce a phylogeny of the organisms and we should be able to identify specific barcodes corresponding to the various clades.

What this doesn't tell us, in the absence of a criterion for defining it, is which of these organisms are of the same species. Clades may be identified at all levels from sub-populations to species and above that through genera and beyond.

To identify a specific barcode for any given population we want a within and between genetic comparison for all of the other populations and organisms available.

To identify a specific barcode for a species we need to have a criteria for what will constitute a species. This can either be based on a previous taxonomy or can be some degree of tightness in the clustering of the genetic markers in the barcodes or some similar metric. Either way that definition will still be arbitrary, which has been the point all along.

Species discovery does not just fall out of DNA barcoding naturally, there has to be a pre-existing species concept for it to hang on.

TTFN,

WK

Edited by Wounded King, : No reason given.

Edited by Wounded King, : retrospective proof reading


This message is a reply to:
 Message 252 by Percy, posted 05-05-2011 10:21 AM Percy has responded

Replies to this message:
 Message 255 by Percy, posted 05-05-2011 11:15 AM Wounded King has not yet responded

    
Percy
Member
Posts: 18364
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.8


Message 255 of 450 (614606)
05-05-2011 11:15 AM
Reply to: Message 254 by Wounded King
05-05-2011 10:46 AM


Okay, thanks, that's clear and makes sense to me, let's see what Al says.

--Percy


This message is a reply to:
 Message 254 by Wounded King, posted 05-05-2011 10:46 AM Wounded King has not yet responded

    
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