Your attitude to numerical taxonomy

I have heard, however, about one problem, however, I have heard, because according to the taxonomy I have only 1 work for myself, still from student times. So, many foreign journals allegedly just often do not take work on taxonomy, where there are no cladistic constructions.I don't know if this is true, but I can reproduce the rumor. And regarding my attitude to the subject - I will add that relying on DNA is IMHO, naive. If, of course, we are interested in evolution, and not abstract "similarity", Because kinship will begin to depend on the size of the genome and other joys.

This post was edited by PVOzerski - 22.06.2006 18: 11

"Of course, if a graduate student starts teaching the supervisor" how to do science correctly " using computers and cladistics, it looks a little strange."
If he starts doing this: why did he go to this manager at all? Doing a job and telling yourself from the very beginning that the topic is bullshit is at least unwise and unproductive. IMHO.

Numerical methods ensure reproducibility of results and at least visible objectivity of conclusions. The conclusions of a classical taxonomist may well turn out to be better than those obtained by numerical methods, but they are practically not reproducible, and the specific mechanism for obtaining them dies along with the classical taxonomist. >

Look through 1000 herbarium sheets, and if you come to the same conclusions, here you will have reproducibility of the result of a classical taxonomist.

< In addition, the matrix is the most visual form of data representation. >

We can agree that the matrix is the most complete form of data representation. But what is the "most visual" - sorry.

< The example with spikes is a classic example of incorrect matrix composition, and numerical methods have absolutely nothing to do with it. >

Exactly so. But... this may be a coincidence, but the cases of successful cladistic constructions known to me were performed by those specialists who first studied the group using classical methods. Again, I do not deny the methods. I am only against 1) their absolutization, 2) the fact that the alleged objectivity of the result guarantees the reproducibility of this result by any amateur who knows how to pull out signs from other people's works and upload them to matrices.

< So, many foreign journals allegedly just often do not accept works on taxonomy, where there are no cladistic constructions. I don't know if this is true, but I can reproduce the rumor. >

There is such a problem (not insurmountable, but still). This, in my opinion, is exactly what is an imposition. Compared to this, the pressure and imposition that we have is just childish babble: -)

< Listen - here's what I don't understand in any way: why in our time build such things as a system and phylogeny based on morphology? There is after all DNA-build on multiple alignments. >

Perhaps in 50 years it will be so. But today it is difficult to call this anything other than "madness". Now molecular methods are at the stage of an early embryo. Sometimes they are already successfully used to solve individual taxonomic issues. But to build systems, wait another 50 years.

< Here, of course, there are also a lot of problems, but at least one of the main shortcomings: which features to add to the matrix and which ones not, practically disappears. >

And in general, the need for a person disappears. Great! After all, a person is a very unreliable link. So, to get an objective result, a person must be eliminated from the study. There are automatic traps all over the planet, from which the material is directly poured into sequencers, processed, and the result is dumped via the Internet to a central supercomputer that builds a system for all living things. Cut all entomologists for nothing. No, leave a couple of them to dust off the supercomputer.

"Perhaps in 50 years it will be so. But today it is difficult to call this anything other than "madness". Now molecular methods are at the stage of an early embryo. Sometimes they are already successfully used to solve individual taxonomic issues. "Of course,
I don't know if you're talking about specific groups or not, but such phylogenies are quite widespread, in particular, I've seen this for nematodes-performed on the basis of multiple alignment of several genes, for drosophila, and probably a lot more. Of course, it is still too early to talk about the construction of an algorithm that allows us to obtain such phylogenies, and most likely it cannot be, but the construction of phylogenies based on molecular data is a reality.

"And in general, the need for a person disappears. Great! After all, a person is a very unreliable link. So, to get an objective result, a person must be eliminated from the study. There are automatic traps all over the planet, from which the material is directly poured into sequencers, processed, and the result is dumped via the Internet to a central supercomputer that builds a system for all living things. Cut all entomologists for nothing. No, leave a couple of them to dust off the supercomputer. "
Uh, no, that's where you're really exaggerating: saying that an automatic sequencer in tandem with databases and algorithms is a substitute for a researcher is like saying that a piano is a substitute for a pianist. These are tools. Getting sequences and aligning them is just the beginning. Of course, to build a sequence tree using such a thing as, for example, clastalW - two minutes and a person does not need to do much, but this, firstly, does not always work, secondly, there are many problems with what to enter into the program, and thirdly... In general, in addition to dusting, there is still a lot of work to do.
PS And why do you immediately talk about the system of all living things? Don't taxonomists build systems for individual types, classes, and orders?..

Listen - here's what I don't understand in any way: why in our time build such things as a system and phylogeny based on morphology? There is after all DNA-build on multiple alignments.

Maybe I will say heresy, but the sequence of nucleotides in a DNA molecule is also a morphological feature, which is no worse, but also no better than other morphological features in their traditional interpretation. Phylogenies based solely on molecular traits are too much at odds with both morphological sensu strictu constructions and with each other to be used seriously to clarify phylogenetic relationships (to date).
When referring to DNA, it is necessary to take into account the unavailability of the DNA of MOST described species on Earth, not to mention the paleontological material, where only morphological sensu strictu constructions are possible.

"Maybe I will say heresy, but the sequence of nucleotides in the DNA molecule is also a morphological feature, which is no worse, but also no better than other morphological features in their traditional interpretation. "
I absolutely agree!!! But why this is heresy is quite obvious... Since DNA is a part of the body and carries information (and what information!)...
Yes, of course, molecular phylogenies are fraught with many "pitfalls", and they can give completely different results for different genes, but if you learn to avoid them , it's up to you to create new algorithms that, for example, could compare protein sequences of distant homologues more subtly than it is possible now or identify regions of them. protein attachment to DNA, and most importantly, be able to determine the importance of a particular position. All this requires data obtained by such "heavy artillery" as microarray (proteins and RNA) and genomics, so from an automatic sequencer to a tree , there is still a lot of sawing and sawing.
"When referring to DNA, it is necessary to take into account the unavailability of the DNA of MOST described species on Earth, not to mention the paleontological material, where only morphological sensu strictu constructions are possible."
Well, I think that the availability of DNA for a much larger number of species than there are now is a matter of the very near future, but with fossils you can't do anything, yes. Then I raise my hands.

What about the sequencing of Neanderthals and mammoths? Do you need links? Very funny phrase " wait 50 years "(this is written by many, and almost exclusively in Russia): everyone will wait, but who will work?

What about Neanderthal and mammoth sequencing? Do you need links? >

As well as sequencing the DNA of dinosaur blood extracted from mosquitoes in Baltic amber :- ) You can also use a scraper to go through the prints on the stones. Paleoentomology is primarily about rocks and amber, not mammoths in permafrost.

< Very funny phrase "wait 50 years" (this is written by many, and almost exclusively in Russia): everyone will wait, but who will work? >

So you can work on these methods. As soon as they become sufficiently advanced, they will start to be used. You will have time to bring it to mind earlier than in 50 years - just say thank you. By the way, I just heard about 50 years from molecular scientists.