NEW BOOK: Snakes of Mexico

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Kelly Mc
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Re: NEW BOOK: Snakes of Mexico

Post by Kelly Mc » July 17th, 2016, 4:13 pm

DNA is morphology on a molecular scale.

The way I see it in my desire to learn things is that science grows on an increasingly finer and finer grid of exploring reality.

Our perceptions can change to understand what becomes known, as it becomes known, or we can just keep believing what has appeal to us ideologically.

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Jeff
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Re: NEW BOOK: Snakes of Mexico

Post by Jeff » July 17th, 2016, 5:55 pm

scottriv

A quick quiz: this snake was found in Mexico last month. What subspecies is it?

Image

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Re: NEW BOOK: Snakes of Mexico

Post by scottriv » July 17th, 2016, 6:05 pm

Jeff,

That is a cute test and I am sure that we could find hundreds of photos of "triangulum"-like snakes that are hybrids of two different sub species or strange color morphs.

All the more reason why counting scales, morphology and locations on a range map really are important to field identification.


Since you appear to be avoiding my question, I will ask it again:

Jeff, does it bother you in the least that No scientist on earth can now accurately identify an animal in the field if we rename everything based on DNA analysis?


And, by the way, I have no problem with using DNA to analyze animals in an attempt to understand them further. I just think we should be using DNA analysis alongside all of the older methods such as ranges and morphology.

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Re: NEW BOOK: Snakes of Mexico

Post by Jeff » July 17th, 2016, 7:08 pm

scottriv

I am not avoiding your question. As you can see from your own post, there is some temporal overlap as we respond to each other.
Jeff,

I did not see your post when I submitted my post up above.
The milk snake photo was a simple illustration of how morphological appearances may not tell us as much as we wish to know about a single specimen. By asking where the snake is from, you are asking to what genetic lineage, or clade, does it belong, rather than identifying it "in the field.". In other words, one submits to the genetics, rather than phenetics, of the animal. I could use the amount of black on the dorsal surface as well as rely on whether or not there was a thiamine or uracil substitution in a particular base-pair of the NAD gene as a key identification character.

You are correct in that the algorithms that systematists use are man-made, but so is the binomial/trinomial classification system. That system forces a pigeon-hole of all animals that exist at this moment in time despite the fact of a transcending continuum of evolutionary processes.

Constructive critique and modifications of existing algorithms will be greatly appreciated, and thanks in advance for any help,

Jeff

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Re: NEW BOOK: Snakes of Mexico

Post by scottriv » July 17th, 2016, 7:17 pm

Jeff, does it bother you in the least that No scientist on earth can now accurately identify an animal in the field if we rename everything based on DNA analysis?

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Kelly Mc
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Re: NEW BOOK: Snakes of Mexico

Post by Kelly Mc » July 17th, 2016, 8:04 pm

It bothers me that you express sexual fascination with a young woman you say you despise.
Its a bad combination.

I advise any young female herper or researcher in your area, never to trust you - and keep that Gerbers handy.

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Re: NEW BOOK: Snakes of Mexico

Post by Jeff » July 17th, 2016, 8:06 pm

locations on a range map really are important to field identification.
You are are correct! Geographic location is often a key aspect in field identification because of the aforementioned spatial lack of genetic manifestation. If I told you where that milk snake was found, you could easily apply a subspecific epithet to it based on geography, but the color pattern would not have helped you. In fact, the coloration may have confused you.
does it bother you in the least that No scientist on earth can now accurately identify an animal in the field if we rename everything based on DNA analysis
Some years ago I took David Beamer to a couple of spots in eastern Louisiana to look for salamanders. At a later spot we found a Dwarf Salamander (Eurycea quadridigitata complex) that, to me, was no different than those we had seen earlier that day. However, David was ecstatic, pronouncing that it was the "western" species. What astounded him was that we were only a few miles apart in a shallow drainage from the "eastern" species. In contrast to your statement, scientists are able to visualize subtle differences as reflected by genetic shifts in species for which they specialize. Similar, minute, or ostensibly invisible character differences were sufficiently apparent to Douglas Rossman in his taxonomic evaluation of western garter snakes, and to David Wake's ability to sort California slender salamanders into 18, rather than 2 species.

Perhaps Dr. Ruane's intimacy with milk snakes enabled her to perceive taxonomic boundaries that you and I have heretofore not discerned.

Jeff

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Re: NEW BOOK: Snakes of Mexico

Post by Jeroen Speybroeck » July 17th, 2016, 11:24 pm

scottriv,

As ever so often, Jeff offered some great explanation. Most of all, he should be applauded to respond in such a civil manner. I suppose it's great that the admin of this forum is so open-minded about mud-slinging, but I guess I'm a European pussy who thinks asking things nicely is more likely to get you your answer than starting with a bang. On this exact same topic (= morphology rules, DNA is evil science), others on this forum, not to mention The Great Hubbs, have also presented ignorance in a coat of arrogance. As far as I've read them, however, none have been as distasteful as yours. Your allegations against the researcher and her promotor are still outrageous to my mind. What's wrong with just asking a plain, neutral question? Not alpha male enough? Seeking refuge in ridicule is also a textbook exit route, of course. And then you went on asking us to convince you that your opinion based on NOT reading the source material is wrong!? Twisted...

But that's an aside now, so 'nough about that! Let me try to be a bit more constructive too.

Of course, we need morphology and range maps. Any decent taxonomic study HAS to include these (and as many other as possible) lines of evidence, imho (and I would agree with you that too often they don't!). Yet, molecular data just may provide more direct insights into the evolutionary history and relationships of taxa. And that's what it's all about - reconstructing the tree of life. Not: creating an easy-to-use morphology-based key. Luckily, both will agree most of the times, though. You could say that taxonomy was created as a labelling system to bring systematic order into living organisms. The (fortunate) shift has however been made to make it about evolutionary history rather than a lookalike contest.

Of course, it is frustrating not to be able to understand and recognize all of it in the field. But is that more important than working with units which represent reproductively isolated units and which actually MEAN something in an evolutionary perspective? You may say "no", but then you're not using taxonomy to reflect that tree of life, and as such, your take on things is outdated, I'm afraid. Just go back 100 years in time, look at the way things were classified back then and tell me if that was any better. Look at how Linnaeus saw the world and you might even have a few laughs. Our means of looking at what surrounds us have become more numerous and more precise, so let's use them?

Of course, any algorithm may be flawed. But isn't that a bit of clincher (had to look this word up, so hope it says what I mean)? Relying solely on morphology definitely is worse, and Jeff provided some great examples on how misleading it may in fact be. The algorithm Jeff explained offers indications for the level of support of the outcome, it's not just some black box. You can question anything, always, but where does that lead you? If your mistrust for (this type of) science is dominant, it's better to abandon any label (species name of whatever) and accept that we are only witnessing a huge soup of genes, at various stages of becoming reproductively and/or geographically isolated units. I'd rather have a system that reflects the relations between taxa/species/clades, based on a "as good as possible" methodology, including all available lines of evidence. That doesn't mean I don't disagree with a LOT of taxonomy papers. Like I said, if US herps would be my forte, I might even disagree with the paper we're talking about and that's not why I responded. But thanks to Jeff we're past that and luckily walked into a much more worthy (and civil, yes, yes) type of conversation.

From Europe with love,

J.

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Re: NEW BOOK: Snakes of Mexico

Post by scottriv » July 18th, 2016, 6:15 am

Jeff,

Now you are telling me that if you are really really skilled, or better yet "intimate" with the snakes, like Sara is with her milksnakes, then and only then will you be able to properly ID snakes in the wild without sending their DNA off for questionable analysis thru human written algorthms of questionable value?

With the old system of classification, anyone who followed the "rules" could ID an animal in the wild.

With today's new and "improved" system of classification, you will now need to become intimate with the animal in order to ID it in the wild.



""Perhaps Dr. Ruane's intimacy with milk snakes enabled her to perceive taxonomic boundaries that you and I have heretofore not discerned.""

Kind of gives new meaning to "Sara's Snake Pit"

https://sararuane.wordpress.com/

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Kelly Mc
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Re: NEW BOOK: Snakes of Mexico

Post by Kelly Mc » July 18th, 2016, 5:03 pm

Thank you for the learning experience on this post guys. There are things that really stick for me, they excite me so I remember easily but other very important subjects have been more of a struggle, and there are posts on this thread that read like a packed little workshop. It made me want to learn more.

I'm getting this book too. Ive got a little OT on my next check ..

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Re: NEW BOOK: Snakes of Mexico

Post by Brian Hubbs » July 19th, 2016, 8:42 am

OK, I was going to stay out of this because almost everyone knows my dislike for the new "rapid-fire genetic" changes done without adequate field study and adequate range assessment in relation to pattern morphs or an adequate number of specimen samples, but after reading all this blather and doing a little assessment of my own I have come to a conclusion: Jeff, Sara, and Burbrink all went to LSU. LSU must be the real problem. If we just eliminate LSU we might have a chance to get back to reality... :lol:

I'm so glad I've become a bird photographer now...

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Re: NEW BOOK: Snakes of Mexico

Post by Jeroen Speybroeck » July 19th, 2016, 10:36 am

Brian Hubbs wrote:OK, I was going to stay out of this because almost everyone knows my dislike for the new "rapid-fire genetic" changes done without adequate field study and adequate range assessment in relation to pattern morphs or an adequate number of specimen samples, but after reading all this blather and doing a little assessment of my own I have come to a conclusion: Jeff, Sara, and Burbrink all went to LSU. LSU must be the real problem. If we just eliminate LSU we might have a chance to get back to reality... :lol:

I'm so glad I've become a bird photographer now...
Finally he bites!!! ;)
And at least your joke was funny.

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Re: NEW BOOK: Snakes of Mexico

Post by Brian Hubbs » July 19th, 2016, 11:34 am

Thanks, but MY jokes are ALWAYS funny... :lol: 8-)

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Re: NEW BOOK: Snakes of Mexico

Post by Brian Hubbs » July 19th, 2016, 12:22 pm


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Re: NEW BOOK: Snakes of Mexico

Post by Fundad » July 19th, 2016, 1:04 pm

Thank you for the post, I think I ll order it tonight and I am looking forward to reading it.

:thumb:

Fundad

Now back to your regularly scheduled taxonomy debating.

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Re: NEW BOOK: Snakes of Mexico

Post by The Real Snake Man » July 19th, 2016, 1:22 pm

Jeff: Just out of curiosity, what kind of milk was that? My gut says annulata but there are a few possible issues with that guess. Where did you find the picture?

-Gene

Edit: found the picture and looks like I was wrong. Welp, just shows to go ya.

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Re: NEW BOOK: Snakes of Mexico

Post by Brian Hubbs » July 19th, 2016, 1:42 pm

Well? What kind is it?

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Re: NEW BOOK: Snakes of Mexico

Post by Jeroen Speybroeck » July 19th, 2016, 2:23 pm


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Re: NEW BOOK: Snakes of Mexico

Post by Brian Hubbs » July 19th, 2016, 2:34 pm

:lol: :lol: :lol:

I can't believe this election... :roll:

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Re: NEW BOOK: Snakes of Mexico

Post by Jeff » July 19th, 2016, 2:52 pm

Just out of curiosity, what kind of milk was that? My gut says annulata but there are a few possible issues with that guess. Where did you find the picture?
Gene

I gather you located the source. A friend of mine, R-man, took the picture last month in northern Yucatan. It is what Hubbs et al. would call Lampropeltis triangulum blanchardi.

Jeff

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Re: NEW BOOK: Snakes of Mexico

Post by Brian Hubbs » July 19th, 2016, 4:57 pm

I wouldn't call it anything because I have no interest in anything from Mexico...and I know nothing about any milks in Mexico. Now, about that LSU problem...

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Re: NEW BOOK: Snakes of Mexico

Post by Jeff » July 19th, 2016, 5:17 pm

Now, about that LSU problem...
Burbrink -- Curator of Herpetology at the American Museum; giant stipend to go catch snakes in Brazil, Madagascar, etc.

Ruane -- Professor at Rutgers University; here is money, go study snakes anywhere in the world.

Boundy -- Louisiana state herpetologist; enough said.

Hubbs -- [crickets chirping]

Hubbs!!! -- [don't wake the crickets]

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Re: NEW BOOK: Snakes of Mexico

Post by Brian Hubbs » July 19th, 2016, 5:54 pm

:lol: :lol: :lol:

Hubbs does just fine, and Hubbs can go wherever he wants, when he wants (within the U.S.-because I have no interest in anywhere else)...the trick is to budget and have two businesses that go on the road with you... :shock:

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Re: NEW BOOK: Snakes of Mexico

Post by Jeff » July 19th, 2016, 6:01 pm

Hubbs does just fine, and Hubbs can go wherever he wants, when he wants
Amen, Brian

In my various conversations and meetings with you over the years I would say that we are the luckiest and most satisfied herpetological enthusiasts out there.

Jeff

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Re: NEW BOOK: Snakes of Mexico

Post by Brian Hubbs » July 19th, 2016, 6:06 pm

Plus, I just started photographing birds last Oct., so now even the time worn places hold new adventure...

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Re: NEW BOOK: Snakes of Mexico

Post by Jeff » July 19th, 2016, 6:21 pm

Hubbs

You ruined it. See my post on cladists...

Jeff

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Re: NEW BOOK: Snakes of Mexico

Post by Brian Hubbs » July 19th, 2016, 6:58 pm

Well, I replied... :thumb:

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Re: NEW BOOK: Snakes of Mexico

Post by DavidSteen » August 12th, 2016, 9:06 am

scottriv wrote:Anton,

In fact, the situation is the exact opposite of what you describe.

I strongly submit that Sara's professor let her get away with all sorts of taxonomic crap that he would have NEVER let his male students get away with.

She wantonly lumped and split a bunch of names that have been around for 150 years and have served science quite well for the entire century and a half.

In the real world, you don't do that without extreme justification and I don't believe that Sara had the scientific justification to do it.

But, as I have said numerous times,,,,arguing taxonomy is like arguing religion. Taxonomy is certainly NOT a hard science and it barely qualifies as a soft science,,,,it is simply a means of labeling species.

What Sara did is in my opinion, an atrocity and I will bet anyone here a beer that her professor has never allowed ANY of his male herp students to wantonly destroy 150 years of taxonomic tradition by lumping and splitting time honored genera the way that she did.

I don't know her professor, but I suppose it is possible that he is not very bright and didn't see anything wrong with her complete revision of triangulum, but my guess is that he was smart enough to know better and allowed it to happen because she is cute and female.

Yea, yea, I am already fully aware of the fact that I am a politically incorrect sexist and it doesn't bother me one iota.
I don’t care what issues you have with Sara Ruane’s research, you owe her an apology for the outrageous, offensive, and inaccurate claims you made about her. If you don’t understand why, your problems are a lot bigger than snake taxonomy.

I’m surprised that some of your comments were allowed to stand by the moderators of this site and humbly suggest to them that they reconsider removing your slanderous and sexist statements.

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Re: NEW BOOK: Snakes of Mexico

Post by scottriv » August 12th, 2016, 2:39 pm

David,

In fact, the more research I have done, the more convinced I have become that using DNA exclusively to do taxonomy is

is close to being scientific fraud.

Ask one of these DNA jockeys why they never assign anything into sub specific groups and you will just get an empty stupid stare.

The reality is that today's DNA analysis cannot distinguish between sub species.

So, if everyone is OK with completely eradicating races and sub specific groupings from all of taxonomy, than using DNA is the way to go.

Do a little bit of studying regarding Epigenetics and then get back to me about how great Sara's work was.

https://en.wikipedia.org/wiki/Epigenetics

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Re: NEW BOOK: Snakes of Mexico

Post by Brian Hubbs » August 12th, 2016, 3:26 pm

David,

I know Scott, and I also agree with his reasoning on this subject. He has brought up some very good points for why DNA classifications do not work well for reptiles. However, I also believe, that like Trump, he allowed his crass and sexist sense of humor to completely derail his good argument and alienate anyone who might follow his train of thought. This is a good lesson for not opening our mouths and then inserting our feet. :lol:

Scott, you are a very intelligent guy. Just argue the reasoning, and leave out the jokes and attacks. I'm on your side and I'd like to see you convey some important info here.

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Re: NEW BOOK: Snakes of Mexico

Post by scottriv » August 12th, 2016, 4:10 pm

Yes, I take back everything crass and sexist I said about Sara. My rude sense of humor often gets the best of me.

But I still maintain that what those people from LA (the state not the city) did to Triangulum is a crime against humanity and taxonomy.

A 30 minute analysis of Epigenetics by anyone with a 110 IQ or higher will clearly explain why DNA analysis alone should not be used exclusively to do taxonomy.

https://en.wikipedia.org/wiki/Epigenetics

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Re: NEW BOOK: Snakes of Mexico

Post by Jeroen Speybroeck » August 13th, 2016, 6:07 am

The reality is that today's DNA analysis cannot distinguish between sub species
Thanks. You wrote one of the most uninformed statements on this forum ever. And that's saying a lot.

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Re: NEW BOOK: Snakes of Mexico

Post by scottriv » August 13th, 2016, 7:42 am

Let me restate this in the most simple way possible.

Current DNA analysis using human derived algorithms cannot distinguish between most currently described sub species.

In other words, if you analyzed 6 different sub species of Lampropeltis zonata with today's DNA testing, all six of the different sub species would appear to be basically the same according to the DNA.

The reason for this is that most of the differences between the different sub species are the result of Epigenetics.

The "Epi" in Epigenetics means "outside", so Epigenetics means "outside" genetics.

You can't use today's flimsy, human written algorithm based DNA testing to test for differences in sub species that are mostly the result of Epigenetics.

If anyone can prove otherwise,,,,give it your best shot.

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Re: NEW BOOK: Snakes of Mexico

Post by Brian Hubbs » August 13th, 2016, 9:13 am

I don't know anything about epigenetics or how DNA testing works, but I do know what certain snakes look like from most regions across the country and how their patterns blend from one to another. When the common kingsnake paper came out I called one of the authors and asked why they had the Desert Kingsnake shown on their map in the drainage of the Little Colorado River in AZ (an area inhabited solely by Cal Kings), and I was told the computer model told them that based on habitat. Well....the computer model was wrong, wasn't it? So, that makes me wonder how much more was wrong with their new species and the rest of their map. I just think it is sad that people rush to accept every poorly researched paper that comes down the pike in the name of science and DNA and computer models, without getting out into the wild to see what is really going on. The late Robert Stebbins felt the same way. At least I am in good company with my opinions.

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Re: NEW BOOK: Snakes of Mexico

Post by scottriv » August 13th, 2016, 11:50 am

Brian,

Because you have 50 years of field experience, you should have no trouble understanding the basics of Epigenetics.

Click the link and within a half an hour, you will begin to see why these DNA jockeys can't tell the difference between a pulchra and a multicincta.

https://en.wikipedia.org/wiki/Epigenetics

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Re: NEW BOOK: Snakes of Mexico

Post by The Real Snake Man » August 15th, 2016, 9:15 am

1. I am not certain that epigenetics are the reason that subspecies look different from one another, and would like to see the scientific research that you are citing for this argument.

2. If that were the case, then there would be no need for subspecific designations, because they wouldn't say anything about the ancestry of the taxa, which is the entire point of taxonomy (clarifying evolutionary history). By your argument, I could release any baby milksnake anywhere in their range and they would do just fine and look like any other milk in their range. And that sounds stupid. Look at what happened to the rossalleni morph of ratsnake after the invasion of the quadrivittata morph.

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Re: NEW BOOK: Snakes of Mexico

Post by Brian Hubbs » August 15th, 2016, 10:57 am

I think the ONLY reason we should retain subspecies is for ease of identification. Yes, subspecies identification can be subjective, but it works better than having one species with five nominal color/pattern morphs in it that just happen to be restricted to their own ranges. Almost all kingsnake species and subspecies will display regional differences in color/pattern, and some will display an array of individual morphs within a subspecies (sometimes mixed in with 5-10 other morphs within the same geographical area, so we cannot call all of them subspecies). But by giving the nominate morph a subspecific name (ie. Pale Milk Snake), we can at least make the ID easier for the novice. Some scientists think ID is not important, but the vast majority of naturalists are not herpers and the new system will confuse the hell out of them. For this reason alone, my books will always retain subspecies names and ranges. I don't care if the DNA jockeys ever buy my books...they aren't written for them anyway... 8-)

All these people have really done is raise some subspecies to species level, and changed the old intergrade zones to new hybrid zones. It's just busy work...it means nothing to 99.9999999999999999% of the human population...but i guess some people need something to do...and sometimes nothing is better than something... :lol:

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Re: NEW BOOK: Snakes of Mexico

Post by Jeroen Speybroeck » August 15th, 2016, 10:36 pm

Looks can be deceiving. Naming living organisms, as a science, is tied to reflecting their evolutionary history and not aimed at creating a user-friendly lookalike contest. Or would you like to lump Morelia viridis and Corallus caninus? You can dislike this, but it is what it is. The alternative seems to each his/her own view of the world.

But I guess we've been there before. Let me also repeat that this does not mean that there's not a lot of ubersplitting going on, so...
Brian Hubbs wrote:I just think it is sad that people rush to accept every poorly researched paper that comes down the pike in the name of science and DNA and computer models...
Agreed! Taxonomic changes without morphological evidence = please no.
Brian Hubbs wrote:... without getting out into the wild to see what is really going on.
But what is "really"? If you only look at external features, you may be mislead on how taxa evolved, and have been or still are interbreeding. If this earns a "don't care" with you, that ends the discussion, obviously.

I am happy that everywhere outside the US no one seems to bother to attribute vernacular names to herp subspecies. It even makes herping the US confusing for me, but I guesss I'm even less than 99.9999999999999999% of the human population (which is anyway already less than 1 person ;) ). But maybe that's also because in Europe we have hundreds of subspecies from before 1900 which one by one turn out to be the result of ubersplitting(!).

Brian, I would imagine it would be easier for a novice to only have to deal with species, and not with subspecies. But that's obviously not my line of thought. It doesn't have to be easy.

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Re: NEW BOOK: Snakes of Mexico

Post by Jeroen Speybroeck » August 15th, 2016, 10:46 pm

I'll add that the new book is gorgeous and offers a wealth of information. Trashing it just because of some taxonomic choices would be a mistake (even though it was written by a European :P).

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Re: NEW BOOK: Snakes of Mexico

Post by Brian Hubbs » August 16th, 2016, 11:24 am

Well, that really just depends on if it was written by a Belgian or not...right? :lol:

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Re: NEW BOOK: Snakes of Mexico

Post by Jeroen Speybroeck » August 16th, 2016, 1:59 pm

Brian Hubbs wrote:Well, that really just depends on if it was written by a Belgian or not...right? :lol:
Naturally! 8-)

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