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Author Topic:   Definition of Species
Percy
Member
Posts: 12821
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.3


Message 168 of 450 (572346)
08-05-2010 10:35 AM
Reply to: Message 162 by Big_Al35
08-05-2010 9:32 AM


Re: Species Definition
BigAl35 writes:

Again I must refer you to a link that I already supplied in another debate about the differences between lions and tigers.

Ok here is one link from potentially many that supports my claim that the differences are hard to distinguish.

I think you will agree that lions and tigers are different species, yet they have almost identical skeletons.

So you think that if we were to dig up fossils of lions and tigers that we might assign them to the same species? While I don't think that would happen with lions and tigers (Wikipedia says they can be distinguished from one another: "However, due to the amount of skull variation in the two species, usually, only the structure of the lower jaw can be used as a reliable indicator of species."), there were probably tons of closely related extinct species that could not be distinguished with only fossil remains. Squirrels come to mind.

Mistaking two different species for the same species happens with living creatures all the time. I presume you don't think it much of a problem for biology when they discovered that African elephants, once thought to be a single species, may actually be multiple species. There's still a debate about this. Yet scientists have no trouble learning a great deal about African elephants.

So why do you perceive it to be a significant problem for learning a lot about, say, T-Rex if we're actually mistaken in thinking our fossils represent a single species? Even if they are multiple species they're still extremely similar.

--Percy


This message is a reply to:
 Message 162 by Big_Al35, posted 08-05-2010 9:32 AM Big_Al35 has responded

Replies to this message:
 Message 170 by Big_Al35, posted 08-05-2010 11:05 AM Percy has responded
 Message 171 by Big_Al35, posted 08-05-2010 11:22 AM Percy has responded

    
Percy
Member
Posts: 12821
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.3


Message 173 of 450 (572413)
08-05-2010 3:20 PM
Reply to: Message 170 by Big_Al35
08-05-2010 11:05 AM


Re: Species Definition
Big_Al35 writes:

We have already discussed three potential definitions of species;
1) genome sequenced definition of species
2) interbreeding definition of species
3) behaviour, diet, appearance, environment based definition.

1 is I believe the newer definition but not yet officially established. TRex fails to achieve species classification by all three definitions.

We have no DNA for T-Rex, of course, but why do you believe that T-Rex fails 2 and 3? Even if our T-Rex fossils represent a genus instead of a species, all that means is that there were more than one interbreeding populations of T-Rex, each population sharing the same behaviors, diet, appearance and so forth, and the several populations being more similar to each other than to any other creatures.

--Percy


This message is a reply to:
 Message 170 by Big_Al35, posted 08-05-2010 11:05 AM Big_Al35 has not yet responded

    
Percy
Member
Posts: 12821
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.3


Message 174 of 450 (572415)
08-05-2010 3:27 PM
Reply to: Message 171 by Big_Al35
08-05-2010 11:22 AM


Re: Species Definition
Percy writes:

Mistaking two different species for the same species happens with living creatures all the time.

Yes, and I bet it happens with extinct species even more. When you have two species that are very similar and then discover a third species which is very similar to the other two, it is easy to fall into the trap of suggesting that the new third species is a common ancestor. This may not be true at all. In the case of lions and tigers a new fossil discovery might be a lion, it might be a tiger, it might be a liger or tigon, or it might be a common ancestor. So there is, in fact, more chance of it not being a common ancestor than of it actually being a common ancestor.

Yes, this is true. Because you cannot distinguish close relations from direct ancestors in the fossil record, scientists will almost never claim that some fossil species represents the common ancester for some later species.

I hope you can see where I am going with this. Enjoy!

If you think you're going somewhere other than a dead end, I can only guess that you think our inability to identify specific fossils as common ancestors means that common ancestors don't exist.

--Percy


This message is a reply to:
 Message 171 by Big_Al35, posted 08-05-2010 11:22 AM Big_Al35 has responded

Replies to this message:
 Message 178 by Big_Al35, posted 08-06-2010 5:46 AM Percy has acknowledged this reply
 Message 180 by Big_Al35, posted 08-06-2010 5:59 AM Percy has responded

    
Percy
Member
Posts: 12821
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.3


Message 185 of 450 (572487)
08-06-2010 6:39 AM
Reply to: Message 180 by Big_Al35
08-06-2010 5:59 AM


Re: Species Definition
Big_Al35 writes:

Here is a link to show that others don't share your view.

Here is a forum guideline that shows how to use links:

  1. Bare links with no supporting discussion should be avoided. Make the argument in your own words and use links as supporting references.

--Percy


This message is a reply to:
 Message 180 by Big_Al35, posted 08-06-2010 5:59 AM Big_Al35 has not yet responded

    
Percy
Member
Posts: 12821
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.3


Message 190 of 450 (572514)
08-06-2010 9:17 AM
Reply to: Message 189 by Big_Al35
08-06-2010 8:48 AM


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

There are plenty of sites showing that DNA barcoding is well underway. Here is a link which shows that some mammals have already been barcoded, and that this is a very effective tool for species identification. I think it's just a matter of time before this becomes the standard. It's not about what I want....it's happening.

You're just not getting what WK is saying, so let's go back to the example I mentioned earlier about African elements. Remember I said that there's a debate about how African elephants should be divided into separate species? Before barcodes for African elephants can be used, decisions must be made about what those species are and how various DNA signposts break down into the different species. These decisions about barcodes are all made by people. Species divisions are a human construct, not a fact inherent in nature.

Some species have little variation and no near relatives making classification as a species an easy task. Other species have a great deal of variation and many near relatives. In such case how does one divide one species from another? Are they different species if they *can* interbreed but don't? Are they different species if they *do* interbreed, but only 0.001% of the time? How about 0.01% of the time? How about 0.1% of the time? 1%? 10%? These decision are all made by people.

Across all the variation of a species, are the different varieties just races within the species, or are they perhaps different species? Within a race is the variation subraces or not? These decisions are all made by people.

Your objections all share something in common: they're all based upon misconstruals.

--Percy


This message is a reply to:
 Message 189 by Big_Al35, posted 08-06-2010 8:48 AM Big_Al35 has responded

Replies to this message:
 Message 192 by Big_Al35, posted 08-06-2010 9:37 AM Percy has responded

    
Percy
Member
Posts: 12821
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.3


Message 195 of 450 (572531)
08-06-2010 10:54 AM
Reply to: Message 192 by Big_Al35
08-06-2010 9:37 AM


Re: Species Definition vs what matters (and why)
Percy writes:

Your objections all share something in common: they're all based upon misconstruals.

Big_Al35 writes:

Objections!?! I don't think I have raised any objections as such...

Really? What about this misconstrual of how much we know about T-Rex:

Big_Al35 in Message 160 writes:

TRex is a mystery. All we have are movie images and directors imaginations to go on. If you found two TRex half skeletons I think you would be hard pushed to even show that it was the same animal. You would have no idea if they could interbreed and their behaviour is unknown.

And what about this misconstrual of DNA's power to determine species boundaries:

Big_Al_35 in Message 177 writes:

I think it's fair to say that species cannot be determined unless you know their DNA.

And what about this objection based upon a misconstrual about scientists claims of finding common ancestors based upon an article you linked to:

Big_Al35 in Message 180 writes:

Here is a link to show that others don't share your view.

And here's you doing the exact same thing again, misconstruing yet another article you linked to about possible scavenging behavior in T-Rex:

Big_Al35 in Message 181 writes:

Here is a link to show that your claim may be very wrong.

Moving on:

Now if our system showed that African elephants were a different species to an Asian elephant then that would be a matter for debate.

Either you misspoke or you're hopelessly confused. While there is debate about how African elephants might break down into different species, there's no disagreement that African and Asian elephants are different species.

By the way, that was you registering yet another objection, right? Just making sure.

If you are saying that experts in the field are actively advocating that Ugandan elephants are distinguished from Zambian elephants and they want them classified as different species I don't have any objection with that as such. Once the system is established and in place we can stick with it.

Species classifications aren't facts of nature like the mass of an electron or the speed of light. They're human constructs. There can never be any gradually homing in on more and more accurate answers because while increasing knowledge always helps the human factor is overwhelming in this case. The very criteria themselves for determining species will change over time. There are probably tons of biologists who don't even take classification that seriously, since it's the actual details that are important and that get lost in broad classification systems.

--Percy


This message is a reply to:
 Message 192 by Big_Al35, posted 08-06-2010 9:37 AM Big_Al35 has responded

Replies to this message:
 Message 196 by Big_Al35, posted 08-06-2010 11:21 AM Percy has acknowledged this reply

    
Percy
Member
Posts: 12821
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.3


Message 202 of 450 (572592)
08-06-2010 5:17 PM
Reply to: Message 200 by Big_Al35
08-06-2010 4:43 PM


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

Yeah...and they all contradict each other.

Can I suggest that unless you have a meaningful point to make that is actually true that you resist the urge to post?

--Percy


This message is a reply to:
 Message 200 by Big_Al35, posted 08-06-2010 4:43 PM Big_Al35 has not yet responded

    
Percy
Member
Posts: 12821
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.3


Message 205 of 450 (573168)
08-10-2010 8:40 AM
Reply to: Message 204 by Big_Al35
08-10-2010 8:18 AM


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

I wouldn't use the word misconstrue...

Al, your middle name is misconstrue.

No one said DNA sequences are arbitrary. Please try again.

I'd love to be more constructive and explain more clearly everything that was wrong in your message, but explaining things to you seems to worsen your understanding. Science attempts to describe reality. If reality is actually different than what science says then science is wrong. If you think evolution is a branch of science that incorrectly describes reality then merely point to the evidence from reality that says it's wrong. Simply misunderstanding what we say time and time again isn't getting this discussion anywhere.

--Percy

Edited by Percy, : Punctuation.


This message is a reply to:
 Message 204 by Big_Al35, posted 08-10-2010 8:18 AM Big_Al35 has not yet responded

    
Percy
Member
Posts: 12821
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.3


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

    
Percy
Member
Posts: 12821
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.3


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

    
Percy
Member
Posts: 12821
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.3


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

    
Percy
Member
Posts: 12821
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.3


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

    
Percy
Member
Posts: 12821
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.3


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

    
Percy
Member
Posts: 12821
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.3


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

    
Percy
Member
Posts: 12821
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.3


Message 257 of 450 (614683)
05-05-2011 9:17 PM
Reply to: Message 253 by Big_Al35
05-05-2011 10:40 AM


Big_Al35 writes:

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 is the gene sets that are unique. Different species can share many of the same genes, but the complete set of genes are unique for each species. The more closely related two species are the more genes they are likely to share, but if they are in reality two different species then one or both will have genes the other does not have. And if you discovered a new species that shared all the same genes as an existing species, guess what? It's not a new species!

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

Yes it would. Looking over the Wikipedia article on the Chimpanzee genome project it appears that we don't really know. Maybe WK can confirm, but I get the impression that while we might know a great deal about some genes, the majority are vague and amorphous and possibly only known to exist by some gross estimation process.

--Percy


This message is a reply to:
 Message 253 by Big_Al35, posted 05-05-2011 10:40 AM Big_Al35 has responded

Replies to this message:
 Message 258 by Big_Al35, posted 05-06-2011 6:46 AM Percy has responded
 Message 260 by Wounded King, posted 05-06-2011 7:16 AM Percy has responded

    
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