Taxonomy as a Rigorous Science

[Dinwar]

Nope, what I did say, and have said repeatedly, is that you don't have enough of a fossil record or DNA to make the assumptions that are made about hominids.

What you don't realize is that what you're saying and what I'm saying you said are the same thing. To say that we can't justify the assumption "These critters are like the other critters in the same group" is to say that we must assume "These critters are different from the same critters in the same group". These are two mutually exclusive working hypotheses--if one is false, the other must be true. And I have repeatedly told you where to find the data. You haven't. Why not? At this point I can only conclude--since you have abandoned all pretense as discussing data or interpretation--that you are incapable of offering evidence to support your side.

Feel free to once again twist that anyway you feel obliged to justify going off on a tangent, that although might be interesting (it was to me), it still doesn't really address what I said.

Jodie, here's the thing: I've addressed what you said. I gave specific references showing exactly what my counter-arguments were using real-world examples that gave you every datum necessary to analyze, critique, and rip apart my argument. Your response? "What do whales have to do with anything?" Why should I waste yet more time providing yet more references when you refuse to acknowledge the nearly self-evident validity of the ones I've already provided?

Once again, you are going off on a tangent not based on anything I actually said.

Yes, I know. I have a habit of thinking about arguments and drawing conclusions from them. You haven't said what I'm responding to, but it is the inevitable conclusion to be drawn from what you HAVE said.

I demand nothing, I stated an opinion.

The terrifying thing is, I believe you. I think you honestly think that declaring, without any knowledge, that entire fields of science you don't even know exist are wrong in specific ways isn't making demands. What that tells me is that you are not only ignorant of the specific data in these fields, but of the process of science.

To say a scientist is in error is to make demands of them. Period. You are demanding they alter their methodology, or defend it--one or the other. The entire enterprise of science rests on the foundation of attempting to define reality. To say that we are failing in a specific way is to demand, as belligerently as humanly possible without actually threatening to harm someone, that we change course or defend our present one. There is no middle ground to statements like those you made; these are not mere differences of opinion. There is no backing down. It may take generations, but eventually only one side will remain--because reality is inherently binary, and when two ideas contradict one another only one can be right. This is serious stuff here. That's why I posted the link about cladistics--they did the same thing you're trying to do, but they did it properly. These people became experts in the field, and when they said something may be wrong they were able to provide example after example--something you have yet to even attempt. I was rather hoping you would take something away from that.

That's my view of what you've done--and yet I've handed you every opportunity to prove me wrong. I have done everything I can to help you. That's because I am FAR more interested in the truth than in a pet hypothesis. I am willing to abandon any hypothesis that doesn't fit the data--but I NEED DATA TO DO IT. You refuse to provide it, and instead have now taken to discussing tone as if that had any bearing on this conversation!

If you like I can quote the insults.

Your take on what I say doesn't change the spirit the statements in which the statements were made. I have not attacked you. I have always attacked your arguments. If you can't differentiate between the two, that's your problem; a scientist learns early on to do so.

There evidently was no argument if you knew that the same methods used for whales, your example, wouldn't apply to hominids.

That is because there's no substantive way in which cetaceans differ from hominids in regards to the methods used by paleontologists. In particular, they clearly demonstrate that your preferred methodology--genetic testing--does not produce significantly different results than morphological testing. You know, the actual topic of this thread? I rather made that clear in the OP (I've no interest in discussing your unsubstantiated speculations regarding hominids--until you have data to support them they are irrelevant).

The taxa are irrelevant; I have only ever attempted to discuss the METHODS in this thread. Your abject refusal to do so in favor of discussing taxa has baffled me from the start. What does the taxa matter if the methods are sound? They work just as well for sponges as they do for whales as they do for ostracods.

The only thing you went out of your way to do was to wave that banner for attention "Look at me, look at me" and some of us have already caught on to that.

Uh-huh. I have two questions for you:

1) Why did I not reference more of my own work? I certainly could have, yet instead I referred to others in the field.

2) Who are those others who believe me to be self-promoting? I can think of one or two (some people simply refuse to accept that when you talk about deep time you need to look at the rock), but I think it fair to ask who these mysterious others are whom you claim to have on your side. Frankly, I don't believe they exist--or, rather, I don't think they've communicated with you about me; I'm too minor a player here to bother with. I think you're lying. And again I've offered you a fool-proof way to prove me wrong.

I'm sure you are speaking from personal experience being on the receiving end of that treatment, this forum happens to provide you with a format to play the other role anonymously.

Actually, I've been on both ends. Believe me, I'm far more vicious when I rip apart people I know. I am very concerned about the sanctity of my field of study, and I frankly don't want screw-ups in it. I've worked too hard and come too far to let some moron who can't read a damn report screw it up for me (no, not talking about you there; it's the reason I gave for failing students back when I was in grad school). And I've actively sought out criticism--I ensure that everything I write goes through at least one other expert (with FAR more experience than me) before it goes to my manager; then HE rips it apart. Then the lawyers do. Then the client does. Then at least one federal and one state agency usually do. Trust me, what I've done to you is only abnormal in that I've been more tolerant than most in my field would be. I am routinely subjected to far worse, and I provide far worse.

And I'm not anonymous; Dinwar is my handle on pretty much everything I do online that allows me to choose my own name, even professional sites. It's as much my name as my real one, far as the internet is concerned. I've used this online handle for more than ten years. I don't give away personal information outside of a very, VERY limited number of friends, but in discussions like this I don't need to; I've been letting the data speak for itself. Again, you haven't provided any.

I would suggest that you follow your own advice.

See, while I have gone against the scientific consensus (it was my first task as a professional paleontologist, in fact), I've always at least made sure that I had a datum or two to support me. In fact, before I go against another scientist I make sure that I'm at least conversant in the major issues in the field--I know the major issues, I know the major players, and I know what sort of evidence is expected from me. So in fact I DO follow my advice. It's rather engrained into scientists by the time they finish their undergraduate work.

There ought to be a way to nominate you for a "body of work" TLA...

Thanks. I do what I can!

 

[Puppycow]

Someone in this thread made comments about the lack of rigor in paleontology, specifically in regards to taxonomy. I made a brief post in that thread, and I'd like to continue my discussion without derailing the thread.

If I may jump in where I more or less left off:

Scientists have an almost pathological aversion to the subjective, and taxonomists are no different. They have established several methods for ensuring objectivity in their analysis.

First and most importantly is the type specimen. This is a specimen (or more rarely a series of specimens) that defines the species in question. The concept is a bit Platonic/"shadows on a cave wall" for my taste, but even I acknowledge that the function it serves is critical. That function is to give a universal and almost always unverying starting point for species determination. Everyone uses the same type specimens for each species; you can't NOT use the same type specimens. These specimens are carefully maintaned in very high-quality labs. The existence of these type specimens does not, I hasten to emphasize, mean that the concept of a species is immutable once established; any time spent reading the taxonomic literature will show innumerable discussions that amount to "This species should be redefined" (particularly now, with the whole Ceratopsian thing going on). Type specimens make the discussion objective because they give us all a starting point, and all the same starting point.

One of the great tragedies of World War 2 was the bombing of so many museums. I'm not trying to deminish the astounding loss of life; I'm just saying that a tremendous amount of scientific data was irrevocably lost. Unfortunately, this was what was required to spur people into routinely including photographs with their species descriptions. Sadly, many pre-war species no longer have type specimens due to them simply being blown up and converted into rubble. I've had personal experience with the tremendous, and sometimes insurmountable, difficulties this causes even today.

The species description is another way to add objectivity. As I said previously, these descriptions are long, dense, and extremely technical. That's because they need to be. These descriptions give us something against which to test our specimens--they in a very real sense are the formal experiment in taxonomy. Once written, anyone can (once they've been trained to comprehend the description) determine if a new specimen is part of that species or not, using precisely the same logic as physicists used to determine if they'd found the Higgs Boson or not. This means that taxonomy is an empirical, experimental science.

Finally, all of the rules for species identification have been codefied in the International Code of Zoological Nomenclature. This is the framework within which taxonomists are required to operate. The Code defines the different types of type specimens (haplotype, paratype, holotype, and a few more that I've never seen in person), as well as how to address synonymies, contradictions, and other issues that will inevitably arise when thousands of researchers contribute to a conversation that's been going on for three centuries. These rules are determined by the researchers for the purpose of ensuring objectivity.

There are some problems with this method, yes. As I said before, it's very Platonic. The type specimen is supposed to represent the big-T Truth of the species, or at least was until fairly recently. This obviously contradicts evolution, and that assumption was abandoned by most researchers a long time ago. At this point, as far as I can tell, most researchers view type specimens as vital conveniences, not as Horse. I know two researchers (three? depends on how you count them--one person is only intermittently part of that team) who are attempting to redefine ammonite species based on population statistics, rather than a type specimen.

Secondly, and far more significantly, the literature is extremely widely scattered. A common type of taxonomic paper is "A revision of the genus ____", in which the researcher puts together everything they can find about that genus and proposes a new understanding of it. A common criticism of such papers is "But you haven't examined THIS paper!" A valid criticism--and drawing such criticisms is one of the critical aspects of such papers. Unfortunately there is no database we can go to to find this stuff. Several have tried to establish one (I think the Tree of Life is ongoing, but I could be wrong), but the task is beyond the comprehension of most. Even putting together all the information on each family within one order is an enormous task beyond all but the most dedicated research teams. What that means is that, unfortunately, when we describe a new species it's often already been described before. Nothing's more disheartening then realizing that your species was already named, back when scientific publications were in Latin (though it does give you a real sense of your connection with the great names in science; referencing Linnaeus is both disheartening and profoundly satisfying).

Another major issue with taxonomy, and in fact the biggest one, is that it does not presume to define evolutionary history. Linnaeus had no intention of discussing--nor, indeed, any knowledge of--evolution. The book "Darwin's Century" discusses some doubts he had later in life, but when he started at least the nested heirarchy was simply a matter of convenience. This is why Arthropoda can be both polyphyletic and a valid taxonomic name--taxonomy, at its start, was merely about putting things in categories. Which means it has a curious side benefit: taxonomy up until very recently served as a truly independent test for evolution. The fact that taxonomy largely matched evolutionary history, despite having nothing to do with it, is very clear evidence that evolution is right.

Still, taxonomy is a powerful tool. And the thing that strikes me about each of these problems is that the people identifying them and addressing them are researchers in the field. Like Creationists, those who attack paleontology for lacking rigor have not, to my knowledge, presented a single criticism that my coleagues and I haven't addressed first, better, in more detail, and found ways to fix.

-------------------------------

In the other thread I had mentioned that the math behind cladograms using morphological characters and genetic characters (characters=traits; don't ask me why, the best explanation I ever got was "Cladists wanted to set themselves apart, and jargon was an easy way to do that). I'm not going to go into too much depth here; if you really want to know more about the math, here is a very good resource. You can also download a freeware program at that site and actually play with some data yourself. Apparently a new version is out; hopefully they made it so you can copy and paste from Excel into it now. That was one of the most annoying aspects of that program. I'd recommend it to anyone who wants to toy with statistics--it can do all kinds of things, from cluster analysis to PCAs to cladograms to simple Gausian statistics. You just have to play around with it until you find out how. It's for serious researchers; they didn't design it to be intuitive to non-experts.

Anyway, here's how the math works, at the 1:1,000,000 scale: You pick your taxonomic groups, and you pick your characters. Genetic taxonomy is easy--you pick the gene, and each codon or base pair represents a character. Morphological data are trickier, but generally by the time you're doing this stuff you've gained a pretty good understanding of taxonomy so it's not too hard. What you want to focus on are shared, derived traits--meaning traits a group has because their ancestor had it and they retained it. Traits that only individual species have are pretty useless for determining evolutionary history--you already know where they evolved, so they tell you nothing. You should also have an "outgroup", a species that is outside the group you're interested in, but close enough to share some primative traits of the group (bacteria are a horrible out-group for primate cladistics; bats aren't too bad, actually). Then you run the program (it may shut down your computer for a while--on a really big database I saw it shut one down for three days).

What the computer does is construct every possible cladogram and count the number of evolutionary changes necessary to arive at that tree. The program will give you the trees with the elast number of changes necessary, on the assumption that the fewer changes necessary the more likely it is that the tree represents the true evolutionary history (as my old professor put it, "We assume that evolution is hard").

What you will immediately find is that there are many. The reason is that the way the heavy math works is by assuming that only pairs are possible--one species splits into two species, but never three or more. Obviously this doesn't represent biological reality; however, the consensus tree--meaning the average of the shortest trees--typically collapses many of the clades, meaning that it groups multiple species together. There is some debate as to what this means; personally, while I haven't run any serious tests of it (I'm still toying with how to run such a test), I lean towards the idea that those collapsed clades represent evolutionary reality: they show organisms that arose from the same stock, if not necessarily the same time.

Now you can test it. There are multiple ways; the ones I'm most familiar with are bootstrapping and jack-knifing. In one (and I always forget which), you simply remove random characters, re-run the analysis, and see what pops out. It does this a thousand times (default setting; you can make it do more). More robust trees can handle the loss of some data; if, however, some structure relies on a single character, it's more likely that it's not real. Often there's a reporting limit of 50% or so, meaning that if the structure doesn't appear on 50% resultant trees, you treat it as if it's not there. The other test also removes random traits, but it duplicates random traits as well--so each analysis has the same number of characters, but not the same characters. It's dealt with the same way.

This is how the math works for ANY set of characters. Genetic or morphological, even behavioral or stratigraphic (yes, I've seen it; no, I do not approve of if)--the characters don't matter, that's how the math works. So in essence, genetic cladograms are not superior to morphological ones.

One thing that's really cool about these trees is that each time the branches come together (called a node), the math will tell you what the traits of that node are. This forms a hypothesis about the nature of the ancestor of those two species. I've found, through analyzing numerous cladograms, that often the cladogram is saying "This species directly gave rise to this other one", which is by itself a really cool concept (I've toyed around with somehow addressing the distance from nodes, but haven't done much with it since grad school; haven't had time or a reason to get back into it). If the node matches a species you analyzed, that means that you are arguing that that speceis gave rise to the other(s) branching off that node. If the node's characters don't match anything you've analyzed, that means you are hypothesizing the existence of an organism ancestral to the ones you studied, and--here's the part that I find unbelievably awesome--you are predicting the nature of that organism. What that means is that someone can go out, find it, and say "Hey, this matches what they predicted"--making cladistics indespensable for making sense of the past. (The researcher would still have to draft a species description and curate the type specimen; the honor of naming the species goes to the discoverer, not to the person who hypothesized tis existence.)

These mathematical methods have been tested. For example, there was a scientist who created a fictional clade of organisms based on a known evolutionary history. He then presented them to scientists and challanged them to reconstruct the history of that clade. Eventually they succeeded--and we've gotten much better at it over time. As an aside, I want to make some of these as stuffed animals for my impending child.

A second test is to compare the hypothesized evolutionary history against what we see in the rock record. We expect some range extensions--FADs and LADs are not usually the first organism to have evolved in that species, but only the first and last APPEARANCE of that species in the fossil record. Still, the fossil record is useful. If you hypothesize a huge number of organisms and we only find three, or hypothesize traits we just don't find, it's cause to re-examine the cladogram, and specifically the characters and assumptions that went into it.

As I said, this is the 1:1,000,000 scale, for all of this--meaning I'm glossing over a huge amount of data and only barely scratching the surface of the stuff I'm adressing. Still, I think it's sufficient to demonstrate the rigorous nature of taxonomy and of our methods for understanding evolutionary history. If anyone would like me to expand on any of these topics, please feel free. And Jodie, please point to specific areas where subjectivity can be problematic.

Yeah, but were you there when the monkeys turned into people?

CHECKMATE ATHEIST!!!1!

 

[Dinwar]

Yeah, but were you there when the monkeys turned into people?

Does watching the new Planet of the Apes movie count for or against me?

I got a chance to read through the paper I linked to yesterday. I'm still working through it--there's a lot of information, and it goes into some pretty lofty stuff (anyone who thinks that philosophy and science don't interact should read the full thing--at one point the author literally starts debating the pros and cons of different types of logic as applied to phylogenies). One thing that I need to dig into more is the section where they discuss various frameworks for determining adequecy of sampling. This directly relatest to this discussion, in that Jodie's entire argument is that we haven't got adequate sampling.

I'm not going to go into it in detail; again, I'm still trying to wrap my head around it. That said, the mere fact that they were able to do this demonstrates the deep flaw in Jodie's position. Paleontologists are well aware of the necessity for ensuring adequate sampling, at all scales; we're also constantly analyzing our techniques to determine if they are adequate or not. The problem I have with Jodie's argument isn't that her points aren't worthy of discussion--they are, which is the whole reason I decided to spin off this thread. My point is that they are being discussed, and have been discussed for centuries. The mere fact that someone in 2000 ce could cite multiple sources on this exact topic is proof of that (I'll grant that it's not proof of the quality of the discussion, but given some of hte names [Gould, Valentine, Jablonski] I'm pretty confident the papers will be well worth the read). The question of adequacy is a facinating one in paleontology, and impacts everything from species identification to Sepkoski's Curve. You can't dangle that big a carrot in front of a bunch of scientists and have us not bite at it.

On a different note, I also saw that my own questions have been previously worked on. One concern I have with cladistics is that it is extremely difficult to determine who the ancestors are in a cladogram--nodes are working hypotheses about ancestrial states. To take the extreme example, if you have every member of a clade to have ever existed--ancestors, offspring, the orginial species, everything--you'd still end up with nodes. That's nonsense; you can't have a hypothesized ancestor if you've got the entire lineage (knowing that is problematic in paleontology, but that's a different issue). Turns out there are methods for dealing with some of that. Most cladograms assume splitting species--Species A gives rise to Species B and C while going extinct. However, you CAN build a cladogram with budding species--where Species A gives rise to Species B and C, but sticks around, so you end up with all three living at the same time. THAT is the model that humans started to follow, which is why our diversity is so high. I've got more research to do before all of my questions are answered, but it's comforting to know that at least that one has been worked on and figured out by paleontologists.

 

[Vortigern99]

Yet again, there has been no acknowledgement from the opposition that she has committed any errors of judgement or fact. Her questions have been answered with no expression forthcoming of her having grasped them; her contrarian position has been systematically dismantled via reams of evidence and professional expertise, garnering nothing but a resonant chorus of crickets.

At first blush Jodie's original question seems reasonable for any student of the subject. I myself, as an undergrad anthropology minor, when introduced to casts of various hominid skulls (laid out on a conference table! ), asked a similar question of my professor: "How do we know that these are distinct species and not variations of the same?" It was the first thing out of my mouth as I sat down to examine the replicas.

Dr. Glassman's response, to paraphrase, was that the observable traits of one skull -- EG a sagittal crest on what was then called Australopithecus boisei (now Paranthropus) compared to the smooth dome of Homo habilis -- were so substantively distinct that they veritably defined the term species. The thickness of the bone of each skull, the prognathic projection of the lower face (or lack thereof), the differences in dentition, the brain capacity, the distance between the eyes, the size of the jaw, and so forth: each trait is unique to its species. To classify them as "regional variations" or "sub-species" is to remove meaning from the word "species", to excise its educative qualities, to stopper its professional practicality.

Dinwar's recent explanation (paraphrasing here) that pre-human hominids were so locally contained that their genotype never had the opportunity to radiate into distinct sub-classifications makes perfect sense. To resist this theorizing -- or fail to address or acknowledge it -- is to demonstrate ignorance of the subject of anthropaleontology, especially without any evidence to support that resistance.

If Jodie has any material basis for her continued refusal to accept the qualified opinions of the experts in an entire field of scientific study, I for one would like to see it. If not, courtesy and the rules of honest engagement dictate that she admit it.

 

[Jodie]

So I ran across this article regarding a new Homo Erectus skull that was found. It states that it might rethink the speciation theory for Homo Erectus, instead, it reflects more variation within the single species. This was what I was referring to when I said I thought paleontology was subjective but I had everything I said twisted around. I'm not admitting that I'm wrong because my point is valid, Vortigen.

http://www.theguardian.com/science/2013/oct/17/skull-homo-erectus-human-evolution

 

[Vortigern99]

So I ran across this article regarding a new Homo Erectus skull that was found. It states that it might rethink the speciation theory for Homo Erectus, instead, it reflects more variation within the single species. This was what I was referring to when I said I thought paleontology was subjective but I had everything I said twisted around. I'm not admitting that I'm wrong because my point is valid, Vortigen.

http://www.theguardian.com/science/2013/oct/17/skull-homo-erectus-human-evolution

Currently under discussion in the "Is this a joke?" thread, which is inadequately titled but contains a robust debate on the Dmanisi remains.

At one point in that thread, Dinwar allows that taxonomy is hypothetical, in that new data and/or new analysis of old data can lead to a reclassification of a given species as a different species or sub-species, etc.

But that reclassification is always based on objective measurements; taxonomy is hypothetical until falsified and then reevaluated. It's not "subjective". Subjective implies arbitrary and/or purely based on irrational, emotional responses and concerns. Taxonomy is rigorous and rational, and you are mistaken in your unsupported contention otherwise.

If you have any evidence that taxonomy is subjective, either zoologically or anthropologically, please present it, because to date you have failed to do so.

 

[The Man]

[slight derail]

Does watching the new Planet of the Apes movie count for or against me?

Against, if you watched it more than once.

I was just moments ago having a discussion with my coworker on the Taxonomy of foxes and where they fall in relation to dogs. I had, just off the top of my head, surmised that they fall into the same family (Canidae) but wasn't sure where they diverge below that. Turns out that they diverge as tribes...

http://en.wikipedia.org/wiki/Tribe_(biology)

a "rank between family and genus" which is apparently below sub-ranks such as sub-families but perhaps leading to even sub-tribes. So sub-family or tribe, perhaps just a sub-tribe. Heck how about a sub-tribe of a tribe of a sub-family of some family. Ones apelike brain could just melt thinking about it too much.

I think I'll just go watch the original Planet of the Apes again, "Damn you, Damn you all to hell!"

[/slight derail]

 

[Jodie]

And I never said it wasn't robust, what I did say was that it is subjective because you can only base assumptions on what you actually have. I did say as other things are found then you change the assumption. You have more information to base that new assumption on, but it is an assumption none the less. If you have a statistically small subset then you don't have enough information to definitively say something is one way or the other and state that as fact.

This was all based on the "table" comment which people shredded. Whether all fossils would or wouldn't fit on a table becomes irrelevant when you compare the number of fossils we have with whatever the existing population might have been across time. I am not incorrect in this point, it was the only point I was trying to make. I have presented more than enough to establish this point so in my opinion this wasn't a discussion.

 

[Vortigern99]

... it is subjective because you can only base assumptions on what you actually have. ... as other things are found then you change the assumption. You have more information to base that new assumption on, but it is an assumption none the less. If you have a statistically small subset then you don't have enough information to definitively say something is one way or the other and state that as fact.

By "assumption" I think what you mean is "conclusion" (IE, based on evidence at hand). By "subjective" I think you mean "hypothetical until falsified, then reevaluated". By "state as fact" I think you mean "consistently choose careful language to indicate possibilities, suggestions and indications rather than asserting incontrovertible fact".

The words you choose mischaracterize what paleontologists do when they classify species using Linnaean taxonomy. To correct your mistaken application of those words, scientists conclude based on data, they don't assume; taxonomy is hypothetical, not subjective; and they use careful language to indicate suggestions, they don't state their conclusions as fact.

 

[Jodie]

But you do use those conclusions as fact when you choose to argue whether bigfoot does or doesn't exist, and that was the bottom line in the "table" discussion as I understood it. I do recall stating that it was a weak argument. The lack of evidence is the strongest argument for bigfoot's non-existence IMO.

 

[Dinwar]

This was what I was referring to when I said I thought paleontology was subjective but I had everything I said twisted around. I'm not admitting that I'm wrong because my point is valid, Vortigen.

Please explain how revising hypotheses to better fit the available evidence is subjective. I'll grant you that this sort of thing demonstrates the fact that all scientific discoveries are subject to revision, but "subject to revision" is nowhere near the same thing as "subjective".

Newtonian physics is objective. It's also very wrong. When we discovered data that contradicted it, we revised parts of it and discarded the rest. This in no way is taken as proof that physics is subjective.

Genetics is objective. It's also, as commonly presented, very wrong. Genes do not produce single proteins, and epigenetic factors can have profound influences on gene expression. When this was discovered, we revised our understanding of genetics--which in no way is taken as proof that genetics is subjective.

Astronomy is objective. Many previous ideas are also very wrong. Exploration of the universe has revised our understanding of black holes, galaxies, planets, even the very definition of terms like "star", "planet", and the like. Yet this in no way is taken as proof that astronomy is subjective.

ALL OF SCIENCE allows for revision in the face of new data, and none of science calls such revisions evidence for subjectivity. In fact, that's what objectivity MEANS: making the best interpretations possible given the data we have. Yet you are demanding that we abandon consistency and the very definition of the term you insist on using for one particular science with which you have some sort of grudge. I'm sorry, but that's insane. Paleontologists are operating in precisely the same manner as every other scientist on Earth. New data was discovered, and we're analyzing our previous interpretations to determine which need revised and which need discarded. THIS IS WHAT SCIENCE IS ALL ABOUT.

If you wish to use a different term to attack the concept of revising hypotheses in the face of new data, you're more than welcome to. But to call this behavior subjective is irrational and an enormous distortion of the English language.

But you do use those conclusions as fact when you choose to argue whether bigfoot does or doesn't exist,

Actually, no. The argument in that thread was that no fossils fitting the description of Bigfoot have been found in the areas where Bigfoot was supposed to live. That is based on the actual specimens (or, rather, their lack), NOT on ANY interpretation. Bigfoot believers provided their descriptions, and no fossil in North America fits them. You are more than welcome to dispute this fact, but in order to do that you need to look at the data: the actual specimens.

The lack of evidence is the strongest argument for bigfoot's non-existence IMO.

Yet somehow the complete lack of any fossil fitting the description of Bigfoot as provided by those who believe it exists does not, to your mind, count as a lack of evidence. I'm at a loss for what else to call it.

 

[Vortigern99]

But you do use those conclusions as fact when you choose to argue whether bigfoot does or doesn't exist, and that was the bottom line in the "table" discussion as I understood it. I do recall stating that it was a weak argument. The lack of evidence is the strongest argument for bigfoot's non-existence IMO.

I'm not a paleontologist authoring a paper on taxonomy or in any way involved in deciding how to classify species. Your contention has been that paleontologists' methods for classifying species is subjective. This thread has shown that is not the case, and you've offered nothing apart from bare assertion to support your opinion.

My conclusion that bigfoot does not exist is based on the same line of evidential reasoning by which one can arrive at the firm conclusion that unicorns, leprechauns, fairies and extant non-avian dinosaurs do not exist. Since I'm not a paleontologist classifying species, my conclusions re: bigfoot are wholly irrelevant to your complaints against the supposed subjectivity of taxonomy.

Got evidence to support your contentions? Great, let's see it. Don't have any? Concede you were mistaken.

 

[Jodie]

Look , once again you miss the point intentionally. When you argue something as fact, using the fossil record as evidence, it is because that fossil record is often changed as things are added that make the argument weak. Conclusions are subjective if there isn't really enough fossils to say definitively, "this is how it evolved". No doubt it did evolve, but probably not in the way it is assumed.

Assumption

1.
a thing that is accepted as true or as certain to happen, without proof.
"they made certain assumptions about the market"
synonyms: supposition, presumption, belief, expectation, conjecture, speculation, surmise, guess, premise, hypothesis;

So if you don't have a large sample then the hypothesis is unverifiable i.e. subjective.

Adj. 1. unverifiable - (of e.g. evidence) not objective or easily verified.
unobjective
subjective - taking place within the mind and modified by individual bias; "a subjective judgment"

 

[Vortigern99]

Look , once again you miss the point intentionally.

Who? Me? Dinwar? Both of us at the same time? How can you possibly know what our/his/my intentions are? Has it occurred to you that we might be disagreeing with you because we genuinely think you're mistaken, and that we're not merely "missing the point intentionally" in order to spite or annoy you?

When you argue something as fact, using the fossil record as evidence, it is because that fossil record is often changed as things are added that make the argument weak.

Okay, opinion noted! Here's my response: We can't draw conclusions from nonexistent data. I'm going to proceed with my life now.

Conclusions are subjective if there isn't really enough fossils to say definitively, "this is how it evolved". No doubt it did evolve, but probably not in the way it is assumed.

Your non-expert opinion as to what constitutes "enough fossils" is irrelevant. "What a statistician/nurse named Jodie thinks is the right number of fossils" is not foremost on paleontologists' minds. You don't have a say in the matter because you lack the credentials and the expertise that would be required before real professionals start paying attention to your complaints. Also, as has been explained to you ad nauseam, scientists employ careful language, theory and hypothesis and indication and suggestion; they don't "say definitively 'this is how it evolved'". You keep ignoring that point for some reason.

Assumption

1.
a thing that is accepted as true or as certain to happen, without proof.
"they made certain assumptions about the market"
synonyms: supposition, presumption, belief, expectation, conjecture, speculation, surmise, guess, premise, hypothesis;

So if you don't have a large sample then the hypothesis is unverifiable i.e. subjective.

Adj. 1. unverifiable - (of e.g. evidence) not objective or easily verified.
unobjective
subjective - taking place within the mind and modified by individual bias; "a subjective judgment"

Thesaurus games are fun! Hypothesis appears as the 10th synonym of assumption. You do realize, don't you, that each successive thesaurus entry gets farther away from the meaning of the original word? That words have discrete definitions, which may overlap with similar words without sharing the exact same denotative or connotative meanings? That a thesaurus groups related words together, not to suggest that they mean the same thing but that they share similar ideas?

You've expressed your opinions time and again without any paleontological evidence or taxonomic examples to support them. This is called bare assertion; it's a logical fallacy. You may wish to consider addressing that before your next screed, rant, tirade, bluster, fulmination, huff, rave, spout,
sounding off, speaking out, speaking up, blaring, blurt-out, bloviation, declamation, haranguing, mouthing (off), oration, pontification, carrying on, rage, storm, or take-on.

 

[AlBell]

Who? Me? Dinwar? Both of us at the same time? How can you possibly know what our/his/my intentions are? Has it occurred to you that we might be disagreeing with you because we genuinely think you're mistaken, and that we're not merely "missing the point intentionally" in order to spite or annoy you?



Okay, opinion noted! Here's my response: We can't draw conclusions from nonexistent data. I'm going to proceed with my life now.



Your non-expert opinion as to what constitutes "enough fossils" is irrelevant. "What a statistician/nurse named Jodie thinks is the right number of fossils" is not foremost on paleontologists' minds. You don't have a say in the matter because you lack the credentials and the expertise that would be required before real professionals start paying attention to your complaints. Also, as has been explained to you ad nauseam, scientists employ careful language, theory and hypothesis and indication and suggestion; they don't "say definitively 'this is how it evolved'". You keep ignoring that point for some reason.



Thesaurus games are fun! Hypothesis appears as the 10th synonym of assumption. You do realize, don't you, that each successive thesaurus entry gets farther away from the meaning of the original word? That words have discrete definitions, which may overlap with similar words without sharing the exact same denotative or connotative meanings? That a thesaurus groups related words together, not to suggest that they mean the same thing but that they share similar ideas?

You've expressed your opinions time and again without any paleontological evidence or taxonomic examples to support them. This is called bare assertion; it's a logical fallacy. You may wish to consider addressing that before your next screed, rant, tirade, bluster, fulmination, huff, rave, spout,
sounding off, speaking out, speaking up, blaring, blurt-out, bloviation, declamation, haranguing, mouthing (off), oration, pontification, carrying on, rage, storm, or take-on.

Spot on.

 

[Jodie]

So basically you don't like the synonyms I used. That's what it boils down to. The next time you try to debate something using statistics then I'll be sure to remind you of what you said here.

 

[Vortigern99]

So basically you don't like the synonyms I used. That's what it boils down to. The next time you try to debate something using statistics then I'll be sure to remind you of what you said here.

No, it boils down to you being demonstrably mistaken in your claim that paleontological taxonomic classification is subjective. Taxonomy employs objective standards drawn from available data; it doesn't depend on biased assumptions arrived at "without proof" <----your definition.

I've never used statistics as a point of discussion in my life. I don't understand it, I'm not educated in that field of study. There's no shame in conceding one's limitations.

 

[Dinwar]

Look , once again you miss the point intentionally.

No, I quite get your point. You want to argue that because paleontologists adjust their hypotheses to fit the data, our hypotheses are somehow subjective. This flies in the face of all evidence, and directly contradicts the definition of the word "subjective".

When you argue something as fact, using the fossil record as evidence, it is because that fossil record is often changed as things are added that make the argument weak.

The fossis record is NOT often changed. The data are immutable and unalterable, with one exception: new data may be added. This is precisely the same as in any other science. An Isotilus maximum from the Silica Shale Formation is from that formation, regardless of whether any additional fossils are found. It cannot be NOT from that formation due to other finds. Similarly, a hominid skull from an African outcrop comes from that outcrop--regardless of other finds. It has particular characters--regardless of other finds. THOSE are the data. Interpretations, such as evolutionary histories, are just that: interpretations. And in science, ALL interpretations NECESSARILY are open to revision.

You've quite neatly set up an impossible situation for paleontology: either we revise our hypotheses in light of new data, in which case we're "subjective" (sensu Jodie); or we do not, in which case you'll call us dogmatic. There is literally no way for paleontologists to handle new data under your scheme.

Conclusions are subjective if there isn't really enough fossils to say definitively, "this is how it evolved". No doubt it did evolve, but probably not in the way it is assumed.

You have yet to provide what you would consider sufficient data to draw conclusions from, despite numerous requests. You have yet to even consider the implications of taphonomy, or the principles of taxonomy, in your rantings. The only conclusion that we may draw at this point is that "enough fossils" is defined as "whatever Jodie says is enough". And that's flagrantly dishonest.

As for the highlighted part, it's a lie. You know better. We do not assume phylogenetic trees; we construct them, and use them as working hypotheses. This is nothing more than an attempt to replace substative arguments--which you don't have--with emotionally charged language in an attempt at a smear campaign. I have explained how evolutionary histories are determined; that's fully half of my OP. If you choose to ignore that it is of course your right, but do not make the mistake of thinking that such an action makes the facts go away. I have addressed this nonsensical claim, and have shown it to be complete rubish.

Assumption

1.
a thing that is accepted as true or as certain to happen, without proof.
"they made certain assumptions about the market"
synonyms: supposition, presumption, belief, expectation, conjecture, speculation, surmise, guess, premise, hypothesis;

I'm sorry, but this is again flagranly dishonest. As I have pointed out, there is no substantive difference between a paleontological hypothesis and that of any other field of science. Thus you are left with two honest options: admitting that you have misspoken, or dismissing ALL hypotheses as mere assumptions. You do not get to call some hypotheses assumptions but not others. There is no way to engage in special pleading and remain honest.

Furthermore, you are ignoring the fact that the term "hypothesis" has different connotations in different areas. In science, a hypothesis is actually fairly rigorous--nothing in science is accepted without evidence (it's not even admissible to the conversation without it), and hypotheses are no different. Look at any seventh-grade textbook on science and you'll see that the first steps to the scientific method are researching the issue--before you formulate hypotheses you need to have sufficient data to justify them. That means that even incorrect hypotheses have SOME evidence supporting them in science! In contrast, "hypothesis" in the vernacular means something like educated guess.

To add to the pile of reasons you are wrong, there is a world of difference between a hypothesis and a WORKING hypothesis. A working hypothesis is more akin to what people think of as theories in science--it's something that has sufficient evidence to be held as true during testing. What I mean is, a working hypothesis has a fair amount of evidence supporting it, and can be used to draw some conclusions; however, it's not fact, and therefore very open to revision, and in fact half the reason to draw conclusions from a working hypothesis is to see of reality matches with those conclusions. Phylogenetic trees are working hypotheses: we can use them to draw conclusions about taxa, and those conclusions can be tested against the rock record to determine if the trees are valid. If the conclusions do not hold true--as may be the case with these hominid skulls--we revise the working hypothesis.

Again, this sort of thing happens all the bloody time. I know people who have made careers out of revising the evolutionary histories of organisms--and I know of at least ten careers waiting for people to decide to take them doing exactly this (not all taxa have been subject to phylogenetic analysis). I won't say that it's the bread and butter of paleontology, but it's certainly a common passtime. The thing is, these adjustments almost always turn out to be minor tweaks that simply don't have profound impacts on our understanding of evolution. The ONLY reason ANYONE outside paleoanthropologists has ANY interest in these new hominid skulls is that we happen to be hominids. There's nothing unique about this paper. And it certainly doesn't undermine paleontology's credibility, any more than altering hypotheses about black holes or planetary formation undermines the credibility of astronomy.

subjective - taking place within the mind and modified by individual bias; "a subjective judgment"

This in no way describes any work in paleontology. The work is objective, as I spent no small amount of time explaining in the OP. You have yet to address any point in the OP in any substantive way. Which SPECIFIC aspects of paleontology take place in the minds of individuals?

The only thing subjective here is your assertion that we do not have sufficient numbers of fossils to draw conclusions about evolutionary histories. It's subjective because there's no evidence supporting it, and you've yet to define what "sufficient numbers" are. We can only conclude that "sufficient numbers" are whatever you say they are--the very definition of subjective that you supplied. So your solution to what you see, in your complete ignorance of the field, as subjectivity is to replace it with actual and demonstrable subjectivity. For my part, I'll pass.

 

[Kotatsu]

First and most importantly is the type specimen. This is a specimen (or more rarely a series of specimens) that defines the species in question.

Can I just jump in, as a professional taxonomist, and point out that despite the misinformation spread by the phylocode people and other children, this is not actually the case. The holotype is most emphatically not some kind of defining specimen, but simply the guarantor that the taxonomist, when he/she describe a species as new, was actually looking at a real specimen, and not just not making things up. It is certainly meant to be representative (1) for what the species in question looks like (i.e., adult specimens are usually preferred, if possible, and specimens that are deformed, incomplete, aberrant, or similar, are typically not selected), but this has nothing to do with defining the species. It is to ensure that the species can be identified by future workers, and that new sets of characters that were left out in the original description (2) can be studied.

I saw that you wrote "The type specimen is supposed to represent the big-T Truth of the species, or at least was until fairly recently." further down, but I just wanted to emphasize that your initial description is not valid any longer.

Sadly, many pre-war species no longer have type specimens due to them simply being blown up and converted into rubble. I've had personal experience with the tremendous, and sometimes insurmountable, difficulties this causes even today.

Sometimes things do not need to be so drastic. The louse genus Zemiodes, for instance, was poorly described by Eichler, but the description included a photo, from which Clay could determine that the purported new species and genus was actually a third instar nymph that was only half-way out of the second-instar exoskeleton. I had the opportunity to look at the type slide (as Clay claimed that the holotype was now "missing"), and as far as I can tell, Eichler unmounted the specimen from its microscopy slide, discarded the specimen, and then added the cover slip back, so that the slide is now entirely empty. Several other slides (non-type material) of deformed lice are in the same drawer, marked Zemiodes?

Sometimes it just takes a bad taxonomist wanting to cover up his own tracks to lose type material. Why he bothered to keep the empty slide at all remains a mystery, though.

---
(1) But, being on my way home from the louse collection at the Museum für Naturkunde in Berlin, I must emphasize that, for some taxonomists at least, any old specimen will be good enough, regardless of how poorly preserved it is...
(2) Again, with reference to the hopeless descriptions emanating from the Berlin museum, that may be virtually all characters... It's very frustrating when someone describes a new genus as "Well separated from the closely related genus X by characters of the head". Of course, Eichler and many taxonomists in the former communist countries had understandable political reasons for doing so...

 

[Jodie]

No, I quite get your point. You want to argue that because paleontologists adjust their hypotheses to fit the data, our hypotheses are somehow subjective. This flies in the face of all evidence, and directly contradicts the definition of the word "subjective".

No it doesn't contradict the meaning of "subjective". How many times do I hear this same criticism applied to other research where the data is incomplete or variables aren't known. The hypothesis based on that same limited data would most definitely be subjective even if you used an objective method to arrive at the hypothesis. The final sum is only as good as the numbers you have to enter into the equation.

The fossis record is NOT often changed. The data are immutable and unalterable, with one exception: new data may be added. This is precisely the same as in any other science. An Isotilus maximum from the Silica Shale Formation is from that formation, regardless of whether any additional fossils are found. It cannot be NOT from that formation due to other finds. Similarly, a hominid skull from an African outcrop comes from that outcrop--regardless of other finds. It has particular characters--regardless of other finds. THOSE are the data. Interpretations, such as evolutionary histories, are just that: interpretations. And in science, ALL interpretations NECESSARILY are open to revision.

Exactly, that was my point.

You've quite neatly set up an impossible situation for paleontology: either we revise our hypotheses in light of new data, in which case we're "subjective" (sensu Jodie); or we do not, in which case you'll call us dogmatic. There is literally no way for paleontologists to handle new data under your scheme.

No Dinwar, I accept the limitations, I think we are looking at this from two different directions.

You have yet to provide what you would consider sufficient data to draw conclusions from, despite numerous requests. You have yet to even consider the implications of taphonomy, or the principles of taxonomy, in your rantings. The only conclusion that we may draw at this point is that "enough fossils" is defined as "whatever Jodie says is enough". And that's flagrantly dishonest.

You are wrong, I provided a mathematical equation that demonstrated what number of fossils would be necessary to have to accurately represent the variation in a Neanderthal population. It doesn't get any more concrete than that.

As for the highlighted part, it's a lie. You know better. We do not assume phylogenetic trees; we construct them, and use them as working hypotheses. This is nothing more than an attempt to replace substative arguments--which you don't have--with emotionally charged language in an attempt at a smear campaign. I have explained how evolutionary histories are determined; that's fully half of my OP. If you choose to ignore that it is of course your right, but do not make the mistake of thinking that such an action makes the facts go away. I have addressed this nonsensical claim, and have shown it to be complete rubish.

I'm not smearing anyone, I'm simply stating that no matter how objectively you obtain your hypothesis, it isn't really all that reliable if the subset isn't representative. It beats nothing, it's not always wrong, but not every species of anything will have a large fossil record and/or DNA to compliment the hypothesis.

I'm sorry, but this is again flagranly dishonest. As I have pointed out, there is no substantive difference between a paleontological hypothesis and that of any other field of science. Thus you are left with two honest options: admitting that you have misspoken, or dismissing ALL hypotheses as mere assumptions. You do not get to call some hypotheses assumptions but not others. There is no way to engage in special pleading and remain honest.

I have not misspoken. I agree that there are limitations like this in every branch of science.

Furthermore, you are ignoring the fact that the term "hypothesis" has different connotations in different areas. In science, a hypothesis is actually fairly rigorous--nothing in science is accepted without evidence (it's not even admissible to the conversation without it), and hypotheses are no different. Look at any seventh-grade textbook on science and you'll see that the first steps to the scientific method are researching the issue--before you formulate hypotheses you need to have sufficient data to justify them. That means that even incorrect hypotheses have SOME evidence supporting them in science! In contrast, "hypothesis" in the vernacular means something like educated guess.

If you are unaware that a hypothesis is incorrect, and build upon that hypothesis, then what exactly do you have?

To add to the pile of reasons you are wrong, there is a world of difference between a hypothesis and a WORKING hypothesis. A working hypothesis is more akin to what people think of as theories in science--it's something that has sufficient evidence to be held as true during testing. What I mean is, a working hypothesis has a fair amount of evidence supporting it, and can be used to draw some conclusions; however, it's not fact, and therefore very open to revision, and in fact half the reason to draw conclusions from a working hypothesis is to see of reality matches with those conclusions. Phylogenetic trees are working hypotheses: we can use them to draw conclusions about taxa, and those conclusions can be tested against the rock record to determine if the trees are valid. If the conclusions do not hold true--as may be the case with these hominid skulls--we revise the working hypothesis.

OK, but the reason it was an incorrect working hypothesis was because the sample set was limited in the first place. That was my point, and my only point.

Again, this sort of thing happens all the bloody time. I know people who have made careers out of revising the evolutionary histories of organisms--and I know of at least ten careers waiting for people to decide to take them doing exactly this (not all taxa have been subject to phylogenetic analysis). I won't say that it's the bread and butter of paleontology, but it's certainly a common passtime. The thing is, these adjustments almost always turn out to be minor tweaks that simply don't have profound impacts on our understanding of evolution. The ONLY reason ANYONE outside paleoanthropologists has ANY interest in these new hominid skulls is that we happen to be hominids. There's nothing unique about this paper. And it certainly doesn't undermine paleontology's credibility, any more than altering hypotheses about black holes or planetary formation undermines the credibility of astronomy.

But it certainly backs up the point I was trying to make about the hominid fossil record now doesn't it?

This in no way describes any work in paleontology. The work is objective, as I spent no small amount of time explaining in the OP. You have yet to address any point in the OP in any substantive way. Which SPECIFIC aspects of paleontology take place in the minds of individuals?

Not every paleontologist agrees with every conclusion. Both camps might have valid arguments for why their point of view is more correct. That is an example of the subjective reasoning involved with interpreting the data that was analyzed using more objective methods.

The only thing subjective here is your assertion that we do not have sufficient numbers of fossils to draw conclusions about evolutionary histories. It's subjective because there's no evidence supporting it, and you've yet to define what "sufficient numbers" are. We can only conclude that "sufficient numbers" are whatever you say they are--the very definition of subjective that you supplied. So your solution to what you see, in your complete ignorance of the field, as subjectivity is to replace it with actual and demonstrable subjectivity. For my part, I'll pass.

Wrong again, I gave you a perfectly good example of a hominid population that was more recent in human history and also has DNA data to compliment the fossil record. If you aren't satisfied with that then I don't know what to tell you.