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Author Topic:   Definition of Species
Dr Jack
Member (Idle past 243 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 34 of 450 (538459)
12-07-2009 8:06 AM
Reply to: Message 33 by penstemo
12-04-2009 11:38 PM


Re: cladistic definition of species?
Despite the growing popularity of cladistics, the traditional Linnaean system is not likely to be replaced in the near future.

I disagree. There are already university's that teach Linnaean classification only as a historical interest. Plus pretty much all recently published classifications use cladistic approaches.

At the Genus-species level, it'll continue, above that it's already broken down. A fixed number of named ranks simply doesn't make sense.


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Dr Jack
Member (Idle past 243 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 36 of 450 (539998)
12-21-2009 1:36 PM
Reply to: Message 35 by herebedragons
12-21-2009 12:23 PM


Re: for herebedragons - speciation, definition first, discussion second
But there are just too many unknowns in the fossil record to be certain that species are categorized correctly. For example, the marsupial flying squirrel and the placental squirrel example you gave me. If fossils were found of these animals they would most likely be considered very similar animals. Like wise the Tasmanian wolf and common grey wolf would be thought to be very close cousins. However, we know they are very different animals.

This is completely untrue. Any trained palaeontologist could easily distinguish a marsupial from a placental mammal because they don't look at crude morphology but at much more taxonomically useful features such as the structure of bones in the skull and the teeth.


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 Message 35 by herebedragons, posted 12-21-2009 12:23 PM herebedragons has responded

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Dr Jack
Member (Idle past 243 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 39 of 450 (540123)
12-22-2009 10:49 AM
Reply to: Message 38 by herebedragons
12-22-2009 10:29 AM


Quality sources
Please use credible sources as opposed to crank websites.

I particular like the way your source neatly elides the difference between "few" and none, and the differences common to all marsupials and features that can be used to distinguish marsupials - that quality quote mining.

Again, my primary point was the difficulty of categorizing extint fossil specimens accurately. So, clearly, there is a large amount of uncertainty in the fossil record.

Yes, there's a large amount of uncertainty in the fossil record, but let's not exagerate the kind of uncertainty or the nature of that uncertainty.


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 Message 38 by herebedragons, posted 12-22-2009 10:29 AM herebedragons has responded

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 Message 43 by herebedragons, posted 12-22-2009 2:50 PM Dr Jack has responded

  
Dr Jack
Member (Idle past 243 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 46 of 450 (540201)
12-22-2009 5:17 PM
Reply to: Message 43 by herebedragons
12-22-2009 2:50 PM


Re: Quality sources
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.

Not all crank sites are creationist. And I was probably a bit harsh; it's not readily obvious which sites are or aren't crank at the first blush - it's one of the joys of the internet. None-the-less macroevolution.net is a crank site promoting a crazy idea cooked up by its owner.

I don't believe I quoted anything out of context. I did edit some content because I felt it was unnecessary to the discussion and sorta lengthy. So I don't see how I am guilty of quote mining.

To be clear I wasn't accusing you of quote mining, I was accusing your source of quote mining.


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 Message 43 by herebedragons, posted 12-22-2009 2:50 PM herebedragons has responded

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Dr Jack
Member (Idle past 243 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


(1)
Message 51 of 450 (540297)
12-23-2009 11:32 AM
Reply to: Message 50 by herebedragons
12-23-2009 10:52 AM


Re: Quality sources
In this case, I really wasn't trying to argue about marsupial identification, but merely trying to point out the difficulties of defining the concept of species.

You're quite right to point out difficulties with identification in the fossil record, you just picked the wrong example. Plants are your best bet, or seaweed. It's not uncommon for different parts of a plant (leaves, seeds, etc.) to end up classified as different species, and the problem is even worse with species that exihibit alternation of generations with very different generations.

This isn't limited to the fossil record, by the way, it occurs even today. Earlier this year a paper was published showing that what had previously been thought of as three species of fish are, in fact, male, female and juvenile of the same species (link.

There's no doubt that such errors of classification have occured in the fossil record.

What are your thoughts about our ability to define and identify the concept of species with a significant amount of accuracy and precision?

The concept of species is not a well defined concept, but it is very useful because it approximates to a natural classification providing you're looking at a reasonably narrow slice of time. It also works pretty well for the kind of large multi-cellular organisms that form the familiar backdrop to our world.

So, in my view, species aren't "real" but they are useful because they describe groups of organisms where investigating the properties of one of that group usefully generalises to all of them, and they are frequently a reasonable level at which to investigate the evolutionary patterns within populations.

I wrote a longer post about this in a another thread: The problem of species

Edited by Mr Jack, : Missing tag

Edited by Mr Jack, : Added link for three fish


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 Message 50 by herebedragons, posted 12-23-2009 10:52 AM herebedragons has responded

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Dr Jack
Member (Idle past 243 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 54 of 450 (540354)
12-24-2009 6:06 AM
Reply to: Message 49 by herebedragons
12-23-2009 10:17 AM


Re: Baraminology
I am not trying to build a case in favor of Bariminology, but I do question the seemingly off-handed dismissal of anything that goes against mainstream science. So many scientific breakthroughs were based on concepts that went against “conventional” thought.

Maybe, although the extent to which science has been advanced by unconventional thought is vastly exagerated, but in every case the area of investigation has been led forward by the evidence. Bariminology, like the rest of Creation Science, does the reverse: it starts with an idea from a position that stands in complete opposition to all empirical knowledge and then starts investigating.

Scientific ideas of populations, clades, and species (ill defined as that concept is) have grown out of empirical investigations of reality; and they've continually tried to form ideas that reflect a natural classification of organisms.

The baramin, as an idea, has no basis in empiricism. The set of organisms you can connect by successful hybridisations does not have any clear link with any kind of natural classification. That's why scientists don't take it seriously.


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Dr Jack
Member (Idle past 243 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 148 of 450 (572176)
08-04-2010 11:38 AM
Reply to: Message 146 by Big_Al35
08-04-2010 9:36 AM


Re: Species Definition
The traditional definition of species is as a group of organisms capable of interbreeding and producing fertile offspring.

No, no, no! A thousand times no!

That's the Biological Species Concept, it's not even close to the traditional definition of a species - dating back only to the middle of the last century. Two hundred years after Linnaeus, yet alone the notion of a species! It's also not a great definition of species anyway.

I've written at length previously about the problems with it. I'll reproduce that post here, to save you clicking a link:

-----

The problem of species

The concept of a species predates Linnaeus, as does binomial naming, but he was he who formalised them and grouped them into Genera, Families, etc. in the familiar system that we still use today. Unfortunately, this system was defined before microscopy, before Darwin's theory of evolution, before Watson and Crick's discovery of DNA and otherwise before the rise of modern biology. It is concept from an age when it was thought that species were the eternal, unchanging creations of God.

We continue to use it because having a grouping for very similar organisms is useful in all sorts of ways and many, many attempts have been made to formalise the concept. They've all failed. The most successful is the Biological Species Concept (BSC), which was originally formulated as "are the same species if they can produce fertile offspring" but later modified to "do so in the wild"1. The BSC has proved an extremely powerful tool for distinguishing species - so much so that many people think it is the definition of species - but it can only be applied to a tiny proportion of currently living organisms.

The vast majority of reproduction on this planet is asexual: all bacteria and all archaea reproduce this way (and just to make things worse they go in for large amounts of horizontal gene transfer) then there's the many eukaryotes that reproduce asexually, both single cellular and multicellular. If things don't reproduce sexually, then the BSC simply can't be applied to them. Most things that have ever lived are now dead, and worse most types of things that have ever lived are now dead. There are countless species that we only known from the fossil record. The BSC cannot be applied to any of the species, because we have no way of telling what they could or couldn't breed with.

So having ruled out the extinct and the asexual, we're left with a small portion of the things we'd like to group into species, probably less than a hundredth of one percent of all living things. But, hey, these species include the big, familiar stuff so that's okay, right? Well.. kinda. Even among the organisms we're familiar with the BSC is hard to apply - you can't, for example, define something as a new species based on a few dead examples or a bit of videos you need to study live specimens in the field, or better yet gene screen a goodly sample - and doesn't actually work all that well anyway. Plants, especially, are particularly fond of forming viable hybrids with different populations we'd really like to describe as different species, and even among the animals creatures like butterflies are alarming fond of merrily hybridising away.

And then you get the crazy edge case hybrids, fish like Poeciliopsis monacha-lucida which is formed by hybridisation of a female P. monacha and a male P. lucida. P. monacha-lucida can viably breed with male P. Lucida but no crossing over occurs, instead the offspring inherit their maternal genome exactly as passed down from the P. monacha, freshly combined with the new chromosomes from the P. lucida sperm. Even whackier is the Amazon molly Poecilia formosa, formed by hybridisation of P. latipinna and P. mexicana. It has to mate with a male Poecilia sp. but the genetic material from that "father" is entirely discarded and the offspring is a genetic clone of the mother. Are these separate species? If not, which species are they? Are they truly a viable hybrid with their crazy forms of reproduction2?

I've concentrated on the BSC here, because it's the idea most commonly advanced as the species definition but I assure that all the other ideas for a definition have suffered from a similar array of problems. There just isn't a single, universally applicable definition of species; instead what is called a species is worked out by on an ad hoc basis by the scientists working in the field using an array of different and varied tools and a great deal of debate. This is particularly true for prokaryotes and fossil species.

To me, this is not surprising, because as I alluded to in my introduction, the concept of a species predates modern biology. The simple fact is that in the light of evolutionary understanding the concept of species is a shaky one as best, perhaps applicable if you view a single snapshot of time, but fundamentally flawed on a longer timescale. The features of organisms within a population change over time (as their genes change), in a way that means that had you a perfect record of these organisms lined up in temporal order it would not be possible for you to point to a particular point where they changed from one species to another but if you looked at the ends of the line you'd find two very different organisms. It is this continuity that makes dividing organisms into discrete species a flawed concept3.

So, in my view, species should not be viewed as a real division of organisms but rather as an idealised tool for understanding the diversity of organisms.

1 - The Biological Species Concept can be defined extremely formally and precisely in terms of gene flow but I think that's a needless complication here.
2 - If anyone's interested these two forms of reproduction are called hydridogenesis and gynogenesis, respectively.
3 - The same problem occurs on a smaller scale with ring species.

Edited by Mr Jack, : No reason given.

Edited by Mr Jack, : Fixing typos


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 Message 146 by Big_Al35, posted 08-04-2010 9:36 AM Big_Al35 has responded

Replies to this message:
 Message 149 by Big_Al35, posted 08-05-2010 5:51 AM Dr Jack has responded

  
Dr Jack
Member (Idle past 243 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 150 of 450 (572273)
08-05-2010 6:02 AM
Reply to: Message 149 by Big_Al35
08-05-2010 5:51 AM


Re: Species Definition
"Fish" is not a species. "Fish" is not even a genus, a family, an order, a class or a phylum. (And "Fish" is certainly not a clade!)

So I'm not sure why you think the fact that ancient fish were also fish is particularly relevant to the question about species.

I am suggesting that the normal definitions of species ie (similar behaviour, type etc and interbreeding and possibly even DNA) are still useful in this case and no snapshot in time is required.

It's your idea that there's a "normal definition" of species I'm objecting to. There isn't. It's not a well defined concept. However, it is a useful one and, I would argue, the best way to apply it is to employ a holistic approach that adopts the various techniques at our disposal so while interbreeding is useful for some, for fossils it has no value, and while morphology is difficult to apply to others, for fossils it's the best (and often only) methodology available to us.

Edited by Mr Jack, : Clean up


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Replies to this message:
 Message 152 by Big_Al35, posted 08-05-2010 6:27 AM Dr Jack has responded

  
Dr Jack
Member (Idle past 243 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 153 of 450 (572277)
08-05-2010 6:34 AM
Reply to: Message 152 by Big_Al35
08-05-2010 6:27 AM


Re: Species Definition
I don't reject the word "fish", I pointed out it isn't a species! It's also not terribly biologically useful because it's paraphyletic.

Shark is better (if you're willing to include the rays as well) because the Elasmobranch group appears to be a monophyletic clade.

It's still not a species though so, again, I find myself wondering what it's relevance to our current discussion is?

These creatures date back 400 million years. I think it's safe to assume that the modern sharks came from these ancient sharks.

No, it isn't. It's safe to assume that modern sharks descended from them or similar creatures living at the same time but it is not safe to assume that those ancient sharks in particular were ancestral. Any more than it's safe to assume an arbitrarily picked Englishman from the 16th century is my ancestor.


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Dr Jack
Member (Idle past 243 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 156 of 450 (572282)
08-05-2010 7:05 AM
Reply to: Message 154 by Big_Al35
08-05-2010 6:51 AM


Re: Species Definition
So, according to you, we should shoe-horn any, and all, extinct animal into a currently extant species? Really?

Where would you put this fella? Or any of these cute little tykes?

The fossil record drips with organisms which are clearly, and indisputably, not a member of any current species. To talk about them as if they are is to hugely distort reality.

The classification of extinct organisms is always going to be more tentative than living organisms, since we have much less data to go on but to suggest we should simply abandon the effort makes no sense to me. How would you suggest paleontologists discuss extinct organisms?


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Dr Jack
Member (Idle past 243 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 159 of 450 (572309)
08-05-2010 9:10 AM
Reply to: Message 157 by Big_Al35
08-05-2010 8:34 AM


Re: Species Definition
No...your putting words into my mouth. I never said this. The best we can do is to identify living species and the known extinct species (like the dodo). Fossils that don't fall into the known categories/species would need another system. I don't know what this system would be...I am not a paleontologist or biologist.

Ah, okay. I understand now

I don't see why you think our existing methods of assigning fossils to species is so flawed? After all the majority of living organisms that would leave fossils could be correctly assigned to a species by their fossils.


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Dr Jack
Member (Idle past 243 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 182 of 450 (572482)
08-06-2010 6:11 AM
Reply to: Message 177 by Big_Al35
08-06-2010 5:20 AM


Re: Species Definition vs what matters (and why)
Your notion that DNA gives a clean, reliable method of determining species is not correct.
This message is a reply to:
 Message 177 by Big_Al35, posted 08-06-2010 5:20 AM Big_Al35 has not yet responded

  
Dr Jack
Member (Idle past 243 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 183 of 450 (572484)
08-06-2010 6:21 AM
Reply to: Message 181 by Big_Al35
08-06-2010 6:07 AM


Re: Species Definition
That would be the evidence of scavenging behaviour...
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 Message 181 by Big_Al35, posted 08-06-2010 6:07 AM Big_Al35 has not yet responded

  
Dr Jack
Member (Idle past 243 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 215 of 450 (574502)
08-16-2010 9:08 AM
Reply to: Message 212 by Big_Al35
08-16-2010 8:28 AM


Re: Pushing back the boundaries of ignorance.
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?

Might I suggest you take some time learning about developmental biology before you make pronouncements about it? We're not speculating about systems we're totally ignorant of here, we're discussing an area of biology about which a great deal is known.


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Dr Jack
Member (Idle past 243 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


(1)
Message 282 of 450 (614946)
05-09-2011 11:13 AM
Reply to: Message 281 by Big_Al35
05-09-2011 11:00 AM


Big_Al35 writes:

Hardly, when chimps and gorillas have a 97% correlation and humans and gorillas have a 97% correlation while chimps and humans have a 98% correlation. Hardly overwhelming.

Phylogenies are not constructed by looking at crude % differences! They're constructed by tracking specific genetic changes.


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 Message 281 by Big_Al35, posted 05-09-2011 11:00 AM Big_Al35 has not yet responded

  
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