Taxonomy as a Rigorous Science

[Dinwar]

My take on this is it depends on what you are using the genetic codes for, be it medical research, forensics, or what have you.

We're talking taxonomy. We have been for weeks. I'm quite surprised that I need to state that again.

Dinwar, I don't think at any point that I screamed my head off,

You may want to re-think that.

but you got rather nasty at times.

~shrug~ You came in declaring that my entire field was incompetent and you were going to teach us how to do Real Science (tm)! without bothering to learn even the names of the fields in question. When I calmly and rationally illustrated some of the serious issues with your argument you ignored them and insulted me. Have I been the epitome of politeness? No. Then again, you've insulted huge numbers of people you know nothing about. I think I've been downright courteous given the provokation. You can of course feel free to disagree--but if you think I've been nasty I advise you to NEVER attend ANY conference involving paleontologists.

In my field, genetic code is considered reliable for research regarding genetic diseases.

Your field is not relevant to this discussion or the one that prompted it. And while genetic codes are reliable for genetic diseases, it's trivially obvious that genetic diseases are not the same thing as taxonomy. Blueprints are fantastic for detecting design flaws--but they suck at giving you driving directions.

I meant in conjunction with genetic analysis.

And now we're back to this.

Just tell me one thing: If you're willing to ignore all of the information in this thread, why should I be polite to you?

I still don't think you can look at ancient hominid skulls, without comparative DNA from those skulls, and get a full picture of who is related to who. So shoot me.

I have no interest in shooting you. However, since you appare impervious to education, I'm at a loss for how to continue. It is obvious to any honest reader of this thread that genetic information is of no better quality--and is in fact often of worse quality--than morphological data. It's obvious to anyone who understands ontogeny and genetics that morphology is going to give you a much wider range of genetic information than standard genetic analysis (ie, morphology looks at a sampling of the whole genome, often admitedly with some extrenuous data tacked on, while genetic studies are often limited to single genes). And it's obvious that with the amount of issues genetic studies have there's absolutely no reason to hold them as better than morphological data--particularly since in at least some cases the results are the same. It's obvious to anyone who understands even the most basic concepts of taphonomy--even such basic concepts as "if you don't have it, it's not there"--that genetic data will always cover less organisms than morphological data will.

I have no idea what to say to someone who can look at all those facts, and more, presented in this thread and still stick to the view that genetic data is somehow better, because reasons. It flies in the face of all rationality.

Implications of what?

And you have the audacity to accuse me of dropping context? Sheesh! The implications of the following quote:

Though this does go to my earlier point: humans are absurdely diverse for a species.

The implication is that humans are weird, and therefore we cannot assume that other species have similar morphological diversity without evidence to support that notion. There are numerous reasons for that. You have completely failed to accept that fact.

I don't know how it works in non-animals (I also tend to ignore plants and stuff...), but I have heard from several sources that the muscles that close clam shells have different mitochondria from the rest of the animal, in that they are inherited from the father, while the mitochondria of the rest of the clam is inherited from the mother. I believe I have heard other examples (Ctenophores?) where the inheritance is from both parents, but I can't remember at the moment. As you say, any hermaphroditic organism may be a good place to start, but there may be other groups.

Humans do inheret some mitochondria from their father. Sperm are basically cells with a nucleus, mitochondria, flagellum, and not much else. Not many mitochondria pass from father to child, certainly not in comparison with the mitochondria in the egg, but a few DO pass on. It's interesting that they're so specifically divided in clams; I wonder what the sorting mechanism is. I mean, at one point they're all in the same cell.

 

[AlBell]

My regards to, in particular, Dinwar and kotatsu for putting the E in JREF. Apologies to others overlooked I no longer recall ids for.

Thank you.

 

[Jodie]

We're talking taxonomy. We have been for weeks. I'm quite surprised that I need to state that again.

I repeatedly said what I was I referring too, I'm surprised I have to restate that.

You may want to re-think that.

No, the only one getting upset here was you as far as I could tell.

~shrug~ You came in declaring that my entire field was incompetent and you were going to teach us how to do Real Science (tm)! without bothering to learn even the names of the fields in question. When I calmly and rationally illustrated some of the serious issues with your argument you ignored them and insulted me. Have I been the epitome of politeness? No. Then again, you've insulted huge numbers of people you know nothing about. I think I've been downright courteous given the provokation. You can of course feel free to disagree--but if you think I've been nasty I advise you to NEVER attend ANY conference involving paleontologists.

No, you read it that way and proceeded to have a come-apart. It was your choice.

Your field is not relevant to this discussion or the one that prompted it. And while genetic codes are reliable for genetic diseases, it's trivially obvious that genetic diseases are not the same thing as taxonomy. Blueprints are fantastic for detecting design flaws--but they suck at giving you driving directions.

As I've said, but it is relevant when you are discussing subjectivity.

And now we're back to this.

Just tell me one thing: If you're willing to ignore all of the information in this thread, why should I be polite to you?

If you are that put out with me then I suggest you put me on ignore. If I took it as serious as you did, I simply wouldn't participate. That would be the normal reaction of someone who dismisses another forum member as not worth the bother.

I have no interest in shooting you. However, since you appare impervious to education, I'm at a loss for how to continue. It is obvious to any honest reader of this thread that genetic information is of no better quality--and is in fact often of worse quality--than morphological data. It's obvious to anyone who understands ontogeny and genetics that morphology is going to give you a much wider range of genetic information than standard genetic analysis (ie, morphology looks at a sampling of the whole genome, often admitedly with some extrenuous data tacked on, while genetic studies are often limited to single genes). And it's obvious that with the amount of issues genetic studies have there's absolutely no reason to hold them as better than morphological data--particularly since in at least some cases the results are the same. It's obvious to anyone who understands even the most basic concepts of taphonomy--even such basic concepts as "if you don't have it, it's not there"--that genetic data will always cover less organisms than morphological data will.

It's obvious to me that you are blinded by the science. If DNA was available for every ancient hominid skull we have on record, I'm pretty certain it wouldn't match the current taxonomy chart based on morphology.

I have no idea what to say to someone who can look at all those facts, and more, presented in this thread and still stick to the view that genetic data is somehow better, because reasons. It flies in the face of all rationality.

I'm not certain that you are rational enough to make that kind of judgement based on this internet conversation but if that's the way you feel I don't think I'll have any problem living with it.

And you have the audacity to accuse me of dropping context? Sheesh! The implications of the following quote:

The implication is that humans are weird, and therefore we cannot assume that other species have similar morphological diversity without evidence to support that notion. There are numerous reasons for that. You have completely failed to accept that fact.

No, I think I accept it just fine. It is why you need both morphological and genetic data to make more accurate charts to reflect the true relationships between our ancestors.

 

[Jodie]

Here Dinwar, all of you, thanks for the educational posts. It might not have had the intended affect but it did change my opinions on some things, just not about hominid taxonomy.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2409102/

Here is an article on fish that discusses underestimating diversity based on morphological data alone.

http://specifyassets.nhm.ku.edu/Ichthyology/originals/sp67152747676086493084.att.pdf

And here is an article that backs up Dinwar's stance.

http://www.utm.utoronto.ca/~w3bio/bio443/seminar_papers/the_role_of_morphological_data.pdf

And one on ants that supports both my opinion and what Dinwar states:

Nevertheless there are some instances where molecular work has confirmed previous morphological circumscriptions of genera. A recent study of the subfamily Dolichoderinae based on 10 nuclear genes generated a strongly supported and well resolved tree (WARD& al. 2010).

Thus, there is a salutary interplay between the two sources of data, with molecular (DNA sequence) data providing the phylogenetic framework whereby morphology can be better understood and more accurately employed for diagnosis and identification of clades.

http://www.myrmecologicalnews.org/cms/images/pdf/volume15/mn15_21-29_non-printable.pdf

So it goes both ways Dinwar, my point of view isn't incorrect, genetics isn't useless in your field. Morphology isn't useless in my field, I used to use it in a sense when judging the likelihood of a successful vaginal delivery by palpating the shape of the mother's inner pelvis in conjunction with the position and descent and of the baby's head to get a mental picture of the overall physics that would need to happen and in what time frame.