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Questions related to Systematics
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I would like to add a data matrix of morphological data, assembled in the software Mesquite, to a manuscript. I would either add an electronic supplement (MS Excel format) or a table as *.txt or *.dic file. Anyone with experience around? I find Mesquite to be a bit user-unfriendly with this regard.
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you can just copy paste the selected range using ctrl+v and ctrl+v as long as the selected range is selected on the mesquite matrix. So for example, if you want to copy a range of 3 rows and 3 columns from the excel, you have to copy that range and go to the mesquite matrix and select 3 rows and 3 columns then paste it.
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Dear all taxonomists
Do you think that the problem which we had with Zootaxa in this year is an accidental or we should expect similar problems in the future? Not only for Zootaxa but also with other taxonomic journals. Do you think that we can do something with it? Any strategy or ideas? Do we have this problem only in zoology or also in botany?
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I don't understand this and similar discussions. There are hundreds of quality journals that publish alpha taxonomy articles in many fields. Why all attention is focused on Zootaxa?
I never publush my research in paid journals because this is a cheating business. However, this does not apply to journals of scientific societies, where member contributions are required.
Here is just a brief list of free quality international peer-reviewed journals (referring in Scopus and Web of Science core collection) that publish articles on animal alpha taxonomy (many of them are with open access; also many journals publish alpha-taxonomy on fossil records):
Zoology/Entomology:
1. Zoosystema (Scopus, WoS core collection) - chargeless
2. Acta zoologica academiae scientiarum hungaricae (Scopus, WoS core collection) - chargeless, open access
3. European journal of taxonomy (Scopus, WoS core collection) - chargeless, open access
4. Zoosystematica Rossica (Scopus) - chargeless, open access
5. Zoologicheskii zhurnal (Scopus, WoS core collection) - chargeless, open access
6. Zoology in the Middle East (Scopus, WoS core collection) - chargeless
7. Invertebrate zoology (Scopus) - chargeless, open access
8. Acta Zoologica Bulgarica (Scopus, WoS core collection) - chargeless, open access
9. Ecologica Montenegrina (Scopus) - chargeless
10. Annales zoologici (Scopus, WoS core collection) - chargeless
11. Arthropod sytematics and phylogeny (Scopus, WoS core collection) chargeless, open access
12. Zoologischer anzeiger (Scopus, WoS core collection) - chargeless
13. Turkish Journal of Zoology (Scopus, WoS core collection) - chargeless, open access
14. Arthropoda selecta (Scopus) - chargeless, open access
Entomology:
15. Annales de la Société entomologique de France, N.S. (Scopus, WoS core collection) - chargeless
16. Insect systematic & evolution (Scopus, WoS core collection) - chargeless
17. Far Eastern Entomologist (Scopus) - chargless
18. Entomological Review (Scopus) - chargless
19. Fragmenta entomologica (Scopus) - chargless
20. Caucasian Entomological Bulletin (Scopus) - chargeless, open access
21. Russian Entomological Journal (Scopus) - chargeless, open access
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Hello Everyone,
The past few years have seen a lot of new cyanobacterial taxa being described using a polyphasic approach. It will be interesting to know that what are the various good things about using this approach and importantly, are there some particular taxonomic groups/clusters that are still unresolved where the polyphasic approach is still to give any proper answer?
What further developments do we anticipate in the coming years? What are the new techniques/methods that can be further incorporated for a better understanding of cyanobacterial taxonomy?
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Although it is not my specialty, I advise you to read the following paper:
A polyphasic approach for the taxonomy of cyanobacteria: principles and applications, by Jiří Komárek (2016).
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A "nursing theory" is a description or explanation of an area of professional nursing. This description or explanation is proposed in a systematic way in order to provide the broadest and most practical information for use in nursing practice and research. They are useful. OK, but it appears that many of them are not practical in a real environment like a hospital or a clinic.
What is your opinion about the obstacles that prevent nursing theories to be practicable? 
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it is perfect questıon,many times I ask this questıon.it can be differnt some country.
İn turkey Health System mıght be obstacle because of.Nursıng shortage,high turnover,hierarchy.
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Can you share any interesting photo concerning butterflies you'd met in nature in your country or during your voyages abroad?
Can you also comment it shortly with a place and date you'd spot it? Also its name. If you are not sure you may ask other participants about the specy name, instead.
E.g.: In May 2019 I'd spend my holidays in Greece, and met there the above Epicallia villica, the cream-spot tiger, a moth of the family Erebidae.
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صورة جميلة لإحدى الفراشات النادرة
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Can you share any interesting photo concerning insects you'd met in nature in your region, country or during your voyages?
Can you also comment it shortly with a place and date you'd spot it? Also its name. If you are not sure you may ask the other participants about the specy name, instead.
During one of my holidays in Dolomiti I've spot the above Panorpa sp. (Mecoptera: Panorpidae) at wild flower of lily in Cortina d"Ampezzo Valley.
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WileyInsect Biodiversity: Science and Society, Volume 1, 2nd Edition
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I'd spend my holidays in Bieszczady mountains, South Poland this late Spring. I'd met a lot of interesting insects there. Could you help me to identify them? What insect is it?
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Dear Prof. Barbara Motyka,
I am interested in bees. So, I have a research paper and a discussion thread. Please have a look at them:
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The recent official publication of PhyloCode has caught my attention, not for new arguments being presented for a system that has already been extensively discussed and, as I see it, whose downsides and problems surpass the envisioned advantages, but surprisingly because of the mediatic coverage it is currently receiving. So many of the major newspapers, which are generally regarded as part of the "mainstream media", are publishing articles and stories praising the "new" PhyloCode as a much-welcome, even necessary, advance to the "terribly outdated" taxonomic classification system currently in use, which "ignores decades of advances in molecular phylogenetics and does not reflect evolutive relationships of organisms". Anyone familiar with the current practices in Systematics is aware that this is malicious disinformation.
In talking with colleagues some have resonated with my impression that, instead of an academic debate, the PhyloCode is becoming a mediatic thing, so that systematists in disagreement with its adoption are branded as "reactionary" and "outdated", not only by the colleagues with whom they disagree but also by the "mainstream media" and possibly the public influenced by it. This type of political interference is negative to Science, and certainly very much unwanted by those endeavouring to advance, improve and refine human understanding of Earth's biodiversity and Natural History.
I think this debate should be kept academic, free as much as possible from this type of political interference. Your thoughts on this topic are very much welcome.
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The success of the Linnean taxonomic system has been its stability. The proof is that the system has persisted for more than two centuries and it is still useful.
Stability was granted because -among other reasons- any change that wanted to be performed on the nomenclatural structure had to be done formally within the academic world.
Paradoxically, it resulted to be a double-edged sword:
1- On the one hand, it enabled communication between researchers, as everybody has to attach to a same nomenclatural framework.
2- But on the other, it really hampered any change, making the Linnean system to look old and rigid.
Turning the ordering of biodiversity in a "matter of opinion" as presented in media is clearly counterproductive. We all must be aware that embracing an unstable phylocode system that tends to name any sister-clades relationship, may have deleterious effect on knowledge transference and mutual understanding.
Now there are a series of journals specialized in fostering formal taxonomic changes. These publications ease taxonomic rearrangements in our raping-changing world, transferring phylogenetic results into manageable taxonomic units, and helping taxonomy to keep up to date.
Let's do not defenestrate what has been achieved over so many years!
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Greetings!
In energy and relaxation calculations, I do a convergence test to determine the best number of K points. I do this by varying the k points number N x N x 1 and getting the energy. When the energy difference between the N x N x 1 and (N-1) x (N-1) x 1 is no longer greater than 0.001 eV, I take (N-1) x (N-1) x 1 as the K points settings.
My question is this: Is there a systematic method similar above in order to determine the best number of k points for DOS calculations? I read in the VASP manual that it should require more k points, but how should I know how many is enough?
Thank you very much.
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Hi,
Step by step process of accurate (both total and projected) DOS and band structure calculations using VASP and some ways of plotting the band structure and DOS of our system is explained in a Youtube video.
The link is:
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For example,
"Taxonomy and Systematics of Molluscs"
or "Systematics of Molluscs"
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Nipu, since the definition of systematics as the systematic classification of organisms (i.e., taxonomy) and their evolutionary relationships encompasses both taxonomy and phylogeny then using "systematics of molluscs" alone would be fine. However, using both taxonomy and systematics would be acceptable by some as well.
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Caterpillars are the larval stage of members of the order Lepidoptera.
I'd met this one on the leaf of basil on my balcony in June.
Can somebeody help me classify this species?
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The caterpillar of the last photo is of Euthrix potatoria (Lasiocampidae).
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(1)Denying the essential differences of infinite set elements’ “special nature, special existing condition, special manifestation and special relationship among each other”, so, elements in all different infinite sets are only heaps of infinite “indiscriminative, nonquantitative, abstract points” and it is unnecessary and impossibale to have any quantitative studying and cognizing on “infinite elements (points) in infinite sets”, the number of elements in all infinite sets are the same and it is just infinite. For example, elements in many infinite mother sets and their sub-sets are in fact all the same stuff of infinite “indiscriminative, nonquantitative, abstract points” without any differences of “nature, existing condition, manifestation and relationship among each other”. The typical cases are “the element numbers in Rational Numbers Set and Natural Numbers Set are equal, the element numbers in Natural Numbers Set and Even Numbers Set are equal and they are just all infinite”. The conclution is: any infinite set has limitless, endlees, infinite elements, so their “one-to-one coresponding operations” of quantitative studying and cognizing on “infinite elements (points) in infinite sets”
can be carried on for ever and their element numbers are all “equally infinite”.
(2)Affirming the essential differences of infinite set elements’ “special nature, special existing condition, special manifestation and special relationship among each other”, so, elements in all different infinite sets can be “discriminative, quantitative visible and tangible mathematical things” and it is necessary and possibale to have all kinds of quantitative studying and cognizing on “infinite elements in infinite sets”. For example, there are different “special nature, special existing condition, special manifestation and special relationship among each other” betwee elements in Real Numbers Set and Natural Numbers Set, so, these two infinite sets have different element numbers. The typical cases are “the element numbers in Real Numbers Set are more than that of Natural Numbers Set, the element numbers in Power Set are more than that of its original set and they are all inequal”. The conclution is: Different infinite sets may have different element numbers. So, in the “one-to-one coresponding operations” of quantitative studying and cognizing on infinite elements of two different infinite sets, the elements in smaller set with fewer elements are consumed and finished soon, it means the element numbers in such an infinite set are not endlees and limitless at all (fake infinite); but in the begger set, infinite many elements are left during this operations, this means its elements are endlees and limitless (real infinite), never be consumed and finished at all, the “one-to-one coresponding operations” here can never be carried on for ever at all.
(3)The above different operating ideas and results of quantitative studying and cognizing on “elements in infinite sets” in present classical infinite set theory are affirmed scientific and both aceptable. The one-to-one coresponding operation idea and result of quantitative studying and cognizing on Rational Numbers Set and Natural Numbers Set is the most typical example. In present classical infinite set theory, on the one hand, we can prove the general acepted conclution of “Rational Numbers Set has exactly same elements as Natural Numbers Set, so it is countable” by the above first operating idea and result; on the other hand, we can also prove “Rational Numbers Set has infinite more elements than Natural Numbers Set, so it is uncountable” by the above second operating idea and result, because just a tiny portion of rational numbers from Rational Number Set (such as 1, 1/2, 1/3, 1/4, 1/5, 1/6, …, 1/n …) can map and use up (bijective) all the numbers in Natural Number Set. This is the newly discoved “’Countable-uncountable’ Paradox of Rational Number Set”. The conclution is: the quantitative studying and cognizing theories and operations in present classical infinite set theory are lack of scientificity.
It is because of the fundermental defects of the absence of “infinite carrier theory” and the unscientific concepts of “potential infinite--actual infinite” in present classical infinite set theory that have been making people unable to know which of the above threedifferent operating ideas and results is scientific and why, unable to know scientifically and systematically the relationship between “elements in infinite set” and “infinite set” , unable to know scientifically and systematically the “nature, existing condition, manifestation and relationship among each other” of sets through their elements, ... This situation has been making people unable to know clearly since antiquity how to carry on quantitative studying and cognizing on elements in infinite set scientifically and systematically, resulting in the production and suspending of all kinds of “infinite things’ quantitative cognizing paradox families” in present classical infinite set theory.
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Five of my published papers have been up loaded onto RG to answer such questions:
1,On the Quantitative Cognitions to “Infinite Things” (I)
2,On the Quantitative Cognitions to “Infinite Things” (II)
3,On the Quantitative Cognitions to “Infinite Things” (III)
4 On the Quantitative Cognitions to “Infinite Things” (IV)
5 On the Quantitative Cognitions to “Infinite Things” (V)
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At this very moment (2 September; 22h00, local time), the National Museum (MN, Rio de Janeiro, Brazil), one of the most important museums of natural history in the world, is burning in flames.
In addition to the exhibitions open to the public, the MN housed some of the largest and most important scientific collections existing in Brazil. The collections of biological items included thousands of types (insects, reptiles, birds, mammals, plants, etc.).
To the taxonomists (and other colleagues): You could say how many specimens (mainly types) collected or described by you were deposited in MN? And to what taxonomic groups (family or above) these specimens belonged?
[In 2016, a coup d’état turned Brazil in a country with no future. Now, in his final months at the head of the Government, the President Michel Temer wants also to ensure that the country erase its own past.]
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I appreciate colleagues for the comments and for the suggestions.
The Brazilian press (newspapers etc.) is biased and shallow and I don’t take it too seriously. On the other hand, article published yesterday (4/9) in The Guardian had the following title: ‘Brazil National Museum: as much as 90% of collection destroyed in fire.’ At the moment, two considerations must be made: (i) this percentage should vary greatly among the different sectors of the institution (from 0% to 100% of loss); and (ii) the fact is that no one yet knows the extent of the losses.
I don’t work in the National Museum (MN) and I don’t even live in the city of Rio de Janeiro. However, a friend of mine who works at the MN sent me today (5/9) some enlightening information (especially about the biological collections), as can be read below:
(1) The so-called Imperial Palace housed most of the collections of the MN. In this building were, among others, the Department of Entomology (except part of Diptera) and part of the collections of mollusks and arachnids. Total loss: collections of insects, including several hundreds of types (e.g., about 1.300 beetle holotypes), in addition to the collections of mollusks and arachnids (but 80% of the types of mollusks have been preserved, because they were in a building annex). The departments of Geology & Paleontology and Anthropology also stayed in this main building. Total loss: the collection of Egyptian relicts (e.g., mummies) and the social anthropology library. However, some items (e.g., meteorites) are being found and collected. The building still housed an electron microscope.
(2) Outside the Palace are the following sectors: the central library; the departments of Vertebrates and of Botany; a small part of Archaeology and some laboratories of invertebrates. All are preserved.
(3) An annex to the Palace (‘Annex Alípio de Miranda Ribeiro’) was preserved. In this building are part of the the sector of dipterology and the collections of invertebrates (except mollusks and arachnids).
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First of all decide what are the equipment, chemicals etc.. required for the project.  procure them, design the work well and systematically carry out the work.  The success is yours. 
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FOLLOWING
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I'd spend my holidays in Bieszczady mountains, South Poland this late Spring. I'd met a lot of interesting beetles there. Could you help me to identify them? What beetle is it?
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The elongate body, long antennae and bright colors suggest that this is a long horned beetle, family Cerambycidae. This is a large family with over 1300 species in North America. These brightly colored adult beetles feed on flowers. Larvae of Cerambycid beetles are wood boring insects and are highly destructive to shade, forest and fruit trees. This particular insect is a locust borer.
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I've heard similar to CNO, but have never seen it tested systematically.
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Thank you Samantha!
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I am doing some research on typifying a plant species and have encountered the following situation.
- The description is very old and no specimens were cited in the protologue.
- No extant specimens survive that would constitute "original material" as defined by article 9.3 of the IUCN.
- The protologue contains an illustration that could be selected as a lectotype , but it is not very detailed and could be variously interpreted as any of several species.
- There are also herbarium specimens of this species collected by the author himself, but years after the description was published, and thus could only be selected as neotypes because they cannot be considered "original material".
My options are the following:
1) Designate the drawing as a lectotype
2) Designate the specimen as a neotype
3) Simultaneously designate the drawing as a lectotype and the specimen as an epitype
I would prefer to select an actual specimen over an illustration which is more ambiguous, but the fact that the extant surviving specimen was collected after the species was published is problematic, and I am not sure if in all cases one should select "original material" over other alternatives that may otherwise be easier to interpret. There appears to be some precedence for option 3 above, but I am wondering what others would suggest in a situation such as the above.
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It is timely to resume this 5-year-old discussion on what is (or is not) a holotype. In fact, the answer then given is no longer correct, due to some relevant changes in th Code approved by the International Botanical Congress in Shenzhen, last summer. efferson, main author of the relevant proposals, should be aware of this. Prior to Shenzhen, Saúl’s answer was the correct one, and option 3 of the original question was the mandatory way to go. An illustration prepared under the supervision of the protologue author could not normally be a holotype, because it could be assumed that the illustrated material was also available for use to that author.
One of the rare example of a holotype illustration I am aware of is the type of Calycanthus praecox L. (nom Chimonanthus praecox (L.) Link), based entirely on a prior illustration by Kaempfer, cited by Linnaeus in the protologue, where he also stated that he had not seen the plant itself (“Ignota mihi”).
What has now changed is the holotype definition (Art. 9.1 of the Melbourne Code), which is no longer restricted to the one specimen or illustration used by the author [of the validating description], but was widened to include “the one specimen or illustration indicated by the author as the nomenclatural type”. This means in effect that, if a single specimen or illustration is mentioned in the protologue it is now the holotype, irrespective of whether or not other elements were available to the author of the description. As from what has been written I take it that in Michael’s original example no specimens were cited and a single illustration was mentioned or provided, that illustration is now the holotype.
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The question stated above is the title of a book review (see http://www.journals.uchicago.edu/doi/pdfplus/10.1086/694936?utm_content=bufferaebfd&utm_medium=social&utm_source=linkedin.com&utm_campaign=buffer ). I thought it would be interesting to read both opinions about the book reviewed ("The Future of Phylogenetic Systematics: The Legacy of Willi Hennig.") and colleagues' own answers to the questions: "Does the Future of Systematics Really Rest on the Legacy of One Mid-20th-Century German Entomologist?"
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The question posed by David Baum in the title of his book review, "Does the future of systematics really rest on the legacy of one mid-20th-Century German entomologist?" is deliberate distortion of our book's title, :The future of phylogenetic systematics: the legacy of Willi Hennig." The book is comoosed of contributions from a Linnean Society symposium that celebrated Willi Hennig's 100th birthday, and it was the organizers' intent to mark his legacy with a book that both looked back at Hennig's historical impact on phylogenetics, and tried to assess how his contributions are still relevant today. All the plesion discussion above is a distraction that has nothing to do with either our book or with Baum's review.
Does the future of evolutionary biology rely on the contributions of one 19th Century English biologist? Does the future of physics rely on the contributions of a 17th-Century English physicist/astronomer? Probably not. But that does not mean that we do not honor the contributions of Darwin or Newton or deny that subsequent work "rests on their legacies." As Newton himself said, "if I see further, it is because I stand on the shoulders of giants."
The fact that people are still arguing about whether or not classifications ought to be based on monophyletic (in the Hennigian sense) groups is a pretty clear indication that Hennig's ideas remain pertinent in the 21st Century.
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Dear Colleague,
I am searching for any possible fellowship to complete my study on Molecular phylogeny and systematic of Sphodristocarabus (Coleoptera; Carabidae; Carabini) species of Iran.
Several species and subspecies of this subgenus described from north of Iran but most of these described species or subspecies synomyzed or their taxonomic status changed, during the time, but the relationship between the species and subspecies of this subgenus in north of Iran, is still unclear.
For example: The subspecies esfandiarii Heinz, 1973, esperanzae Heinz, 1970 and morvani Morvan, 1976, first time placed under species adamsi Adams, 1817, but later Lassel (2001), put these subspecies under species bohemani Ménétriés, 1832.
So it is my pleasure if any body can suggest any possible fellowship to complete this study.
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The DAAD (Deutscher Akademischer Austauschdienst) offers grants to this kind of projects, usually for no more than 6 months in German Universities. There are several types of grants, so, you must look in the DAAD website for further information. The process is competitive and you must be in contact with a German professor in advance, which support and approves your project (a support letter is compulsory before to apply). If you do not have the support letter of acceptance by a German professor, your application will not be accepted.
Good luck!
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What do you consider the most important developments in the fields of Systematic Conservation Planning and/or Integrated Spatial Planning over the last 5 years?
Additionally, are there techniques/tools/technologies that facilitate the application of these newer developments? What are your favorites? What works well? What doesn't?
References/citations welcome :-)
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In your data, do you see any systematic trends in shifts toward heavier isotopes of Nickel?
Thanks very much. Lew
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Ok, I could not resist looking at the slides already. I have really tons of questions. Could we continue this discussion through email?
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Hi
One of the statistical analysis that usually is done on DNA barcoding sequences is calculating CG-content. I read in some papers that this sequence (COI or cox1) is usually AT rich in insects. But I didn't read about the importance of this observation in discussion part on the article.
I'm aware of the application of CG-content in systematics of bacteria, but what about Eukaryota like insects?
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Bacteria have been living on earth a few billion years longer than the Metazoans, and some of the bacteria evolved to live in very extreme environments such as hot thermal vents or ice. The mitochondria are essentially one lineage of bacteria that live within eukaryotic cells and within any sublineage of eukaryotes such as insects there is not so much diversity in nucleotide composition bias as there is across all bacteria.
The CoxI gene of insect mitochondria averages 69% A+T and 31% G+C while the CoxI gene of mammal mitochondria averages 58% A+T and 42% G+C. It is possible that the higher G+C content in mammals is due to a warm blooded lifestyle, but I am not sure if that is proven.
Anyway, the AT/GC ratio in a group of metazoans such as the insects or the mammals is quite stable and not a major factor to consider when barcoding species within such a lineage.
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I found that Weiyong Lu (China University of Mining Technology) systematically steal papers from me and many others.
My research topic is plasma based acceleration, and this guy steal many of my highly cited papers ( including Nature papers). how can I deal with this kind of cheater more efficiently?
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Dear Wei, as your names are quite similar, I assume that you mean that he is listing your papers in his researchgate profile, correct? If so, I would get in touch with the researchgate team.
Best regards,
Robert
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I am finishing a paper about Knowledge management and I would like to describe Brazilian context in a systematic way. Looking for ideas.
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Knowledgement in Brazil
Please let me know if these references/sites are useful to you:
1. Knowledge Management and e-Government in Brazil
Knowledge Management and e-Government in Brazil Page 2 of 11 Introduction In a study much-cited in Brazil (OECD, 2003, p. 8), the Organization for Economic
2. Knowledge Management Analyst at Brazil - UNcareer
https://uncareer.net/vacancy/knowledge-management-analyst-114271
Knowledge management in UNDP is guided by a Knowledge Strategy that enables UNDP Brazil to share and leverage its knowledge and experience across government, private sector, civil society, UN agencies and other external partners.
4. The use of knowledge management practices by Brazilian
Regarding knowledge management, the review of knowledge management practices of Baskerville and Dulipovici (2006) was used, in addition to other articles which analyzed these practices and the relation of knowledge and firm performance (Audretsch & Keilbach, 2007; Bembenek & Piecuch, 2014; Bender & Fish, 2000; López-Nicolás & Meroño-Cerdán, 2011; Mills & Smith, 2011; Mosconi & Roy, …
5. Knowledge management consultants in Brazil - knoco.com
https://www.knoco.com/knoco-brazil.htm
Knoco Brazil Knoco in Brazil is headed by Fabio Batista, Brazilian citizen and resident in Brasília since 1977, and KM Manager at Summit Quality Systems Consultores Associados, a consultancy specialized in knowledge management, strategic planning and quality management.
Dennis
Dennis Mazur
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It would be better if the article mentioned the properties of acids
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Dear Sir,
You can use American Public Health Association (APHA) standard methods books for the same.
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The ABAT Accreditation and ACM Computer Science Curriculum is systematically evolving and adapting to make sure that current and future Computer Science Graduates are well trained and qualified to enter the job market with proper skills and competencies. Is the current or future ABAT Accreditation adopting the new developments in Bio-Computing, and to what extend will both the undergraduate and graduate higher education change in next five years?
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Thank you Saif. With current dynamic research, innovation and technological advancement of Computing Technologies side by side with Bio-Technologies and Bio-Computing, is it critical to adopt and update the Computer Science and Engineering Curriculum to match the industry expectations from graduates as future potential employees.
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I would like to know who is the author of this definition and these 6 theory analysis steps ?
"Theory analysis is the systematic examination of the
theory for meaning, logical adequacy, usefulness,
generality, parsimony, and testability."
SIX STEPS IN THEORY ANALYSIS
􀁼 identify the origins of the theory
􀁼 examine the meaning of the theory
􀁼 analyze the logical adequacy of the theory
􀁼 determine the usefulness of the theory
􀁼 define the degree of generalizability and the parsimony of
the theory
􀁼 determine the testability of the theory.
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The original six-step approach was from the 1988 second edition of the same Walker and Avant book. They added two steps in later editions.
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if anybody have idea where i download this book, thanks you very
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Send me your e-mail, I can give you library access to an electronic version of all three parts of the book (i.e. Part A, B, and C).
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If you have to chose between two sampling methods, Consecutive sampling or systematic random sampling for your study, from the hospital OPD, which method is better. As in fixed duration say from Jan 17  to Dec 17, if we do by systematic random sampling ie we chose one patient from first five and then chose every fifth patient then the systematic random sampling is only representative of consecutive samples, hence I feel that the consecutive samples should be better. Need advice and clarification from researcher
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Completely random would be the best choice. All available experimental units get a number, and a random number generator identifies the participants. Alternatively, randomly select 200 days in a year, and randomly select a time. Take the first experimental unit to arrive after that time. While slightly different, these two approaches should give you very equivalent results.
This is not always possible.
Say that the experimental units arrive one at a time.
1) You could flip a coin and heads you are part of the study, tails you are ignored.
2) You could roll a 6-sided die. The first roll is a 4, so you take the fourth person through the door, and then roll again. The roll is a 3, so you take the third person. And so forth.
3) You could sample on Monday. Randomly select a time interval. Say 3pm to 6pm. Within this time interval take the first 100 people and randomly select 30. Do this for the other days of the week.
4) Randomly select a day of the month, a day of the week, and a time interval. Everyone in that time interval gets sampled. Do this again next month.
Of course it is much easier to sample by going out and taking the first 273 experimental units that are close to you. However, this may give you a population that is very different than your intended target. The hospital "samples" one part of the larger human population. Some hospitals are affluent, others not so much. A hospital in McAllen Texas might get more Hispanics compared to a hospital in Jerusalem. Bus schedules might shift patient profiles or the work schedules of the people in your area. Doctor schedules would also be influential. Dr. Bob is on vacation the week you sampled, so you miss many of Dr. Bob's patients. Randomizing your sampling improves the chance that your sample applies to the population at large, rather than some minor subpopulation.
Warning: random sampling is not exactly what you want. I have 3,000 experimental units. I randomly select 200. It is possible (though not very probable) that I will get the first 200 experimental units. You might get the first 100 experimental units and the last 100 experimental units. These must be taken if you are using a random number generator and claiming that you used random sampling. Otherwise you have a "random sampling design that was biased by all the possible combinations that you didn't like." It might be more honest to maximally disperse your sample through the population (every 15th experimental unit). There is nothing random about this approach, but it avoids the shady side of claiming randomness when you don't accept a large number of the random possibilities.
You can also consider an experiment on experimental methods. Based on a large number of factors I can only sample once. I will sample the first 200 experimental units on Monday starting at 8:00. That is my experiment. It produced some interesting results. Now I go back and sample on Wednesday at 3:00 and collect another 200 experimental units. Do I get the same result? I'll do this again, and again to get 50 such experiments. It took a couple of years to do, but now I have a good idea of how that particular design interacts with the people arriving at the hospital. I can combine the data to understand the larger population. I can then advise if this is a good strategy for future work. I am also confident that my results are not an artifact of one sample of 200.
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Deer taxonomy
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no, only fragmentary materials are known, and to my knowledge, practically nothing was described, other than by Sickenberg 1975, and the only complete antler from Megalopolis that was preserved (but never depicted / described!), has recently been destroyed during the June 2017 earthquake on Lesvos, unfortunately (the museum was damaged).
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Accounting for core gain and loss after every run offers a reliable basis for sample evaluation thus strict core quality standards need to be maintained  at all times. How then can one account for core loss or gain ? Is there a systematic manner to tackle this ?
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One issue is the logging of the along-hole depth of the cores themselves.  This is usually done based on driller's depth (defined by drill pipe) during the drilling process, and is often not clearly matched to wireline depths against which petrophysical and geological parameters are logged. This can be addressed using "way-point" driller's depth measurement which then arrives also at an uncertainty for the depth measurement. This  allows measurement correlation to be done based on comparison of not only the features themselves but the uncertainty of the measured depth values.  See me for details, if this is of interest.
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Any evidence supporting the use of systematic desensitization/ stimulus control to manage cataplexy symptoms?
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Thank you for your replies. There seems to be a consensus that CBT is helpful for narcolepsy. It will be great to know if there are any studies looking at the effectiveness of behavioral intevention for cataplexy.
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How do a computer main board start up?
When you press the start button on a computer what procedures happen to turn on the CPU.
In another way, a CPU has a DC-DC converter to supply own variable power needs. But what things I want to know are a systematic procedure of turning on a CPU.
Thank you in advance for whom giving me guidance.
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Mohamad, I would not say the mainboard starts up but the whole computer instead, because that process includes not only the mainboard but also the power supply, the BIOS, the CPU, the I/O system, etc.
When you press the "start button", the first thing that is activated is the Switched-mode power supply (SMPS), that converts the typical/domestic 110/220/240V AC (depending on where you are) to 12V DC, then this device activate the flow of 12V DC to the mainboard, and when the Central Processing Unit (CPU, which is of course connected to the mainboard) detects this voltage (12V DC) it automatically executes the program encoded in a memory called Basic Input Output System (BIOS), which performs a number of tasks, such as the Power On Self Tests (or POST, for checking memories, I/O system, etc), and then looks for the Master Boot Record (MBR) on a preset I/O device, for booting the operating system that this piece of code within the MBR is pointing to.
Broadly speaking, that is the process. I suggest you to look for more information searching for "booting process" and/or any of the acronyms that I have used here.
I hope that helps. Best regards.
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Dear all,
What do you think about the revision of the GUM? Do you know if we will soon have another version of the Guide and what, according to your knowledge/experience, will change or should be changed?
Do you think that the concepts of random and systematic uncertainties will be used again? What then about Type A and Type B uncertainties?
Regards,
Biagio
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Dear Biagio, as far as I know, there will be some major revisions. The basis of the Uncertainty Approach should not be changed, however, its application will be revised. For instance, the propagation of distributions (Monte Carlo) will be the primary choice to determine measurement uncertainty using a modeling approach. Accordingly, the alculation of coverage interval will no longer depend on degrees of freedom evaluated using the Welch-Satterthwaite formula. So, the use of degrees of freedom will be considered as an out-dated vision. This pseudo-revolution already happened in the field. Another is the primary use of 3s instead of 2s on the reported outcomes. Like I'm a senior researcher in the medical laboratory, I hope the International Federation of Clinical Chemistry and Laboratory Medicine (IFCC) allow this document to be understandable by the laboratorian. For instance, using some GUM supplement.  I also hope GUM could have a section oriented to the use of empirical models based on experimental data - that's what matters to the med lab! The concepts of Type A and Type B errror should be kept, however, there should happen some changes related to the use of the degrees of freedom.
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Since cladistics and then cladism were born in Western Germany and then developped in English-speaking Western countries, I am interested in the perception of this classificatory philosophy in the former Soviet Union before 1991 and then in its successor states.
I make a carefull distinction between the methodology of tree reconstruction called cladistics, and the dogma that all taxa must be holophyletic called cladism. I do not want to discuss whether cladism is right or wrong here, I am only interested in the perception of scientists in these countries (now and historically).
I am interested in your own testimonies, but I am also interested in historical papers I could read since I didn't find anything myself.
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It is a very interesting – and still underexplored – research topic. Generally, the Soviet taxonomists were rather hostile towards cladism (= phylogenetic systematics). Hennig’s classical book on foundations of cladistics is still not translated into Russian, and the first benevolent surveys of this taxonomic phylosophy did not appear in the USSR until the late 1980s. Of course, now the situation is quite another. Cladistic methodology is accepted by anybody who wants to use it, and it is almost impossible to find a theoretical paper written in Russian to reject cladism as a ‘wrong’ methodology. However, most taxonomists of old generations are still working within pre-Hennigian paradygm. But I would like to place your question in a wider context. Generally speaking, any attitude towards cladism concerned with a problem: “should phylogeny be taken as a foundation of the system?” I have to note that there was a long tradition of decoupling taxonomy and phylogeny on theoretical basis in the Russian taxonomy. As long ago as in the 1920s, some prominent systematists of Russia insisted that the phylogeny cannot serve as the basis of a system. I mean chiefly zoologists since I am not very familiar with the works of Russian botanists on this subject. Some of these Russian authors who rejected phylogeny published not only in Russian. I’d recommend you to read two papers of Eugene Smirnov, a very interesting Russian theorist of taxonomy:Smirnoff E.S. 1924. Probleme der exakten Systematik und Wege zu ihrer Lösung. Zoologischer Anzeiger, 61: 1-14.
Smirnov E.S. 1925. The theory of type and the natural system. Ztschr. indukt. Abstannmungs- und Vererbungsiehre, 37: 28-66.
These texts contains explanation why the ‘phylogenetic taxonomy’ is wrong (according to Smirnov).
Another prominent Russian author of that time, Vladimir Beklemishev, also insisted that systematics must not use phylogenetic data at all. Unfortunately, his theoretical views were not published in language other than Russian.
Concerning the post-Hennigian time, the most articulated theoretical work aimed to bring arguments against cladism is:
Skarlato O.S., Starobogatov Ya.I. 1974. Phylogenetics and the building of a natural system. Trudy Zoologicheskogo Instituta AN SSSR, 43: 30-46. (in Russian only).
Discussing Hennig (1950), the authors conclude that his attempt to reform taxonomy “leads to a complete elimination of taxonomy as a scientific discipline” (Skarlato & Starobogatov, 1974: 32). I may add that Starobogatov was among the most influential theorist of taxonomy in USSR, and his methodological views have been read widely.
Well, it is a top of iceberg, of course. If you like to get more information about the Russian theoretical taxonomy (very peculiar and very interesting if to view it in comparison with the Western European thinking), please ask me more. I am sure that the hostility towards cladism in the Soviet taxonomic community has deep philosophical roots and cannot be viewed as a over-simmplified picture of ideological confrontational between ‘East’ and ‘West’.
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For example the study is conducted through the interview and systematic observation. Can I use just interview part in my systematic review?
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Not so straight forward as the accumulation of logic which occurs in systematic reviews. I agree with Aled's observations over the strength of mixed methods. We recently had similar issues and opted for including quantitative results into a systematic review, and qualitative into metasynthesis?
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How can i determine if an amblypygi is a male or a female using its morphological appearance?
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Hello,
as Gustavo already said correctly, it is not that easy. Beside some obvious sexual dimorphism you have in same species “hidden” ones, e.g. all female specimens of the genera Phrynichus, Euphrynichus and Damon have red hairs on the posterior margin of the genital operculum. I also found this in some Charon spp. from the Philippines.
Beside this, I did it often in past, but stopped it completely in the last years: narcotize the specimens gently with CO2 and lift the GO carefully with a fine, thin needle and check it. You need some experience for this, but it is not a big deal.
Beside this, I do it now always “via feeling” after breeding thousands of thousands specimens, but this is of course no good advice for you, but what you can do: take the exuvia after molting and check the sex. You see the same structures and can sex them without any impairment.
Regards,
Michael
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Sadly collecting location is uknown, but possibly Indonesia. I assume one of the two species being D. sumatranus.
very thankful for any help.
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I think is a female of the variable species draco sumatranus Schlegel, 1844.
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Tardigrada and Bdelloidea research in México is very limited, so I would like to identify researchers or grups on these topics to make a network. I work mainly on systematics of Tardigrada and Bdelloidea groups. 
Thanks for your answers
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I work with bdelloids. I would be glad to try to help you.
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does it make sense to investigate the systematics of a specific region, for instance the systematics of stag beetles of Japan, or the systematics of weevils of the Landkreis Hinterratzenreute?
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If one sees taxonomy and systematics as different things, then my answer would be no. On the other hand, a taxonomic revision of the species living in Australia would certainly be a useful thing to have. It all depends on the aim of the work.
However, in the cases I am aware of, the Australian fauna is very deceptive and phylogenetically important. With this I mean that there are formerly unrecognized world-wide groups and relict types that have contacts to many directions. A phylogenetic analysis of these without previous (or simultanious) knowledge of the world fauna is not that great an idea.
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Identification requested to experts. Currently i am working in high altitude plant ecology at Great Himalayan National Park, Kullu, India. i want to identify these four plant species from the above mentioned study area from an elevation upto 3400m above sea level.
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Picture 2: Cardamine - Brassicaceae
Picture 3. Androsace - Primulaceae
Picture 4. Stellaria - Caryophyllaceae.
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Lately I have studied Toyota Manufacturing System, but it seems I go in circles, because the tools are so intertwined, sometimes so overlapped, that I cannot let go one tool while studying another one. I go round and round, it gets me boring. I think that the System as a whole is a masterpiece, but when it comes to be studied under systematic methods, it seems so redundant. I feel like wasting tons of times, and I get in the same place of the beginning. Because you need to link the dots between and among tools to make sense of this whole thing. So, my question is: how can one study Toyota System tools, as a self-learner, harnessing the study time as best as possible? (I consider that this study lacks practice, so in this sense I rise my question, as a newbie in this subject.)
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Dear Eric 
Thank you so much. I think you hit the nail, it is all about to avoid losses, wastes, time. Nevertheless, there are so many other approaches out of Toyota tools that address such goal of losses avoiding. Some are new one, as Manufacturing 4.0. And other are old one. As those linked to cleaner production, eco-efficiency etc. Also, I have found articles that highlight disadvantages of lean production in terms of the avoidance/elimination of intermmediary stocks, mainly in cases of supply chain disruption. I have found several examples of losses in Toyota, Nissan, and Seagate facilities in Thai during the 2011 floods in that country. There were mentioned losses due to lack of intermmediary stocks because the suppliers could not delivered raw materials during such natural disaster. Actually any system or theory work under limitation.
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Where there are slight differences it often becomes very difficult in traditional/classical taxonomy to separate varieties (forms), subspecies, sister species or cryptic species especially where reproductive isolation or behavioural or other differences are difficult or impossible to see.I am in the habit of separating geographic variants as subspecies and sympatric variants as varieities/forma. However, I have read some comments on Researchgate that all geographic variants should be regarded as separate species while I believe that such differences if minor should be looked at as incipient speciation. Orshould it be left to the specialist to decide whether a taxon should be treated as a variety/subspecies/different species as Darwin suggested? 
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Classic taxonomy works well in deeper nodes where species no longer interbreed.  For cases with speciation in progress, DNA, ecological, and behavioral studies are needed to understand why, from who,  and how much the populations have diverged. We often don't have those studies in hand while needing to give a name to a new form.  So, we use classic taxonomy, but need to keep in mind that the name and placing of that form may change as new studies come along.  I see the use of morphological taxonomy in species that are being formed as a temporary placeholder.  
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We currently working on wolffish larvae hatched from wild-caught eggs and at ca 180 dph we're still not sure to which species they belong. Hopefully, we'll see this later in the juvenile/adult phase.
However, for similar, future work it would be extremely valuable if we can determine at the onset of the experiment, to which species the larvae belong.
Any information on genotyping/bar-coding procedures appreciated.
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Another and possibly cheaper and faster option would be to develop species-specific primers, and run the PCR-product on a gel to see which of the primers worked, an thereby identify the samples. Then one can start with the samples in the morning a nd get the answer the same afternoon. 
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I have not come across any paper where it is systematically stated about how to calculate life cycle impact of a product manufactured using any process. if any one has idea or paper, kindly let me help in this regards,
Thanks with regards,
Janak Valaki
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I request brethren from the research and academic community to answer the following question. What is the procedure of writing a manuscript (article/ note/ short communication, whatever it be!) dealing with rediscovery/ new report or extended geographical report of any taxa, be it plant, animal, fungal or lichen?
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Taxon rediscovery, extended geographical report or new report all are very subjective and the researcher only may judge the genuinity of his finding.  If he/she is confident about his finding it can be communicated as an article/note or short communication to an appropriate journal in their prescribed format. Each journal may also have yardsticks to measure the manuscript appropriate for them. Finally researcher can find an appropriate journal and publish.   
To clarify it, there is no specific criteria for time span, area of distribution etc for any of the above category.  What is the interval to be considered for a rediscovery from previous record?  What is the spatial difference  to consider it as a new geographical report or a new report?  (one can claim new report for an adjacent district/ an adjacent state or even a country).
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The aims are to know relationships among individuals in one species and to classify into two groups: good and bad individual which will be used to increase a population and to control it.
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If you look for overall correlation between morphological and genetic data for the same sample set, you shold perform Mantel test. All you need are the distances (or similarities) between the accesions. I would suggest R package ade4 to do this.
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Collected from the coastal waters (benthic domain) of the Bay of Bengal, please help me identify the specimens. Anyone? Guess these are teatae amoeba!
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Dola:
Well I can guess that your image in frame 1 resembles a thecate Amoeba. In frame 2 resembles cyst of a dinoflagellate. See link:
Best
Syed
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We found this mantis and ootheca during a herpetology expedition this spring in eastern/central part of Kyrgyzstan (Naryn region). Unfortunately we have a problem with determination. Any suggestions are welcome. Any tip for papers engaged in distribution data of Mantodea in Central Asia would be also very appreciated.
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Allright, thank you. I found out that it is on the Red List of Kazakhstan which surprised me. Still can not find any relevant info about KG though. Do you know any russian-written papers?
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Politically skilled but otherwise incompetent people might sometimes climb up the ladders of an organization better than people high on substance know-how but low on politics. This, of course, likely results in non-optimal management performance. It would be interesting to know if there's a systematic bias involved here.
Anyone know of this type of research?
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The attached article discusses when and how sociopaths rise rapidly in the managerial ranks and examines their destructive impact through incompetence and self-serving behaviours. I think this might what you're alluding to in your question ...
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Olfactometers allow for the systematic administration of odorants to humans. I'm looking for something similar (preferably commercially-available and computer-controlled) for tastes/liquids.  I've looked around, but so far, I haven't found anything.  I'm trying to avoid making my own if possible! :-)
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Hi Thomas,
Please check the link for the gustometers.
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This question was edited since it made absolutely no sense, owed to my previous inexperience with the topic.
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Either that, or construct your tree by any other means (RaXML, MEGA, PHYML, PAUP, Mr.Bayes), and then use any of the R packages. I recommend you stick to likelihood-based methods (either frequentist of bayesian), rather than distance measures such NJ.
Best
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I think it might be Elmidae or Eulichardidae.
Thank for you help
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Dear Vincent Lefebvre
I agree with your opinion on this taxon. I got a few information about Coleoptera larvae, in Neutropical, i know they are not in same, Neutropical and Oriental. 
Anyway, thank for your help, Vincent Lefebvre. I'll get further discussions with my teacher and i think that we can go further in the identification. 
Best wishes!
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I have generated category summarized taxonomy tables, alpha and beta diversity metrics in Qiime and want to present the data in good publication quality graphical images. Are there any alternatives to Qiime generated output?
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hello everyone ! I got a question about trait evolution analysis.
I have COI (Cytochrome oxidase I) DNA sequences for all species, and I have excel sheet for all morphological characters for all species eg. (thorax volume, proboscis length, wings and legs length, Max. width of tergite and sternite, mature egg length and number of mature eggs in ovary.........ect.). I need to use R software (ape and caper package).
Now, I want to analysis these data to study trait evolution history (Mapping these traits on the tree, the evolution relationships between these species). So, how could I achieve that goal ?
thank you all ! Any comments would be appreciated !
actually, I am a beginner in this field, I didn't have a lot experience. I need to now that:
1- I should build the tree from different software (like MEGA) and then import this tree to R.
2- Can I import the sequences to R and build the tree from it with out use other software?
3- In which kind of format I should save the sequences to import it to R?
4- how can I link this morphological data to the tree?
Thank you for all.
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Aram, when you say that you want to "analysis these data to study trait evolution history" by "Mapping these traits on the tree" you are predefining the relationships according to the sequence data as if the morphology carried no valid phylogenetic signal. Its a very widespread practice, but has no scientific validity. You could compare the sequence and morphology trees and see where they match. Where they do not match you have a problem for which there is no objective recipe to solve.
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I am trying to use Polysat to perform calculate pair-wise distances and determine Principal analysis (PCA) on a polyploid (hexaploid) group. To do this in polysat we use the command code "> plot(pca[, 1], pca[, 2], col = rep(c("red", "green", + "blue"), each = 100), main = "PCA with Bruvo distance")" is used. In this code the term "each = 100" specifies the number of samples in each population (group). The assumption here is that populations have equal number of samples. My question is how can this term be modified in order to accommodate populations with different sample numbers? I would appreciate any suggestion that would help me address this issue?
Thank you 
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You can try like this "PopInfo(simgen) <- c(rep(1, 100), rep(2, 71), rep(3, 101))"  or PopInfo(simgen) <- rep(1:3, c(100,71,101)).
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Estimation of ageing errors while determining precise age from different ageing structures. How errors are calculated while estimating precise age in fishes.
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You can control systematic error with the proper model of sequence evolution - use some model choice program to help you identify the best model. However, because sequence evolution follows a Poisson process, the random error (standard deviation) with increase with time back to the common ancestor (mean) and will always be quite large (a Poisson mean equals the standard deviation), Nevertheless you do have control over reducing the systematic error so do that at least.
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It seems that the taxonomic ranks subfamily and tribe are not commonly used in current bacterial systematics. Here are some of my findings. The LSPN (List of Prokaryotic Names) website does not include names at the subfamily or tribe rank. The NCBI bacterial taxonomy also does not have these ranks. Tindall et al. (2006) specifically remarked that "The ranks of subfamily, tribe, subtribe and subgenus are not widely used at present." I did a quick Google Scholar search for the tribe name "Pseudomonadeae" and only found 76 results, of which only 13 since the year 2000. See the attached links for the relevant info.
This is quite curious to me. The International Code of Nomenclature of Bacteria actually specifies rules for forming subfamily and tribe names, among other ranks such as family and order.
In my view intermediate ranks such as subfamily and tribes increase the resolution and informativeness of a classification and should be used. These ranks are very commonly used in zoology and botany.
What do you think are the reasons subfamily and tribe are not used and what is the relevant history?
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In addition to the difficulty of resolution with bacterial taxa, sub-families and tribes are not always present in other groups of organisms either. For instance, some plant families have tribes (Asteraceae) or sub-families (Fabaceae), but many do not have either, and none have both.
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Attached is a pretty picture of what our current understanding of species looks like at the genome level (ie the big complete picture)
Generally the darker the colour the better the match between isolates.
This particular picture is of all the currently known genome sequenced isolates of S. epidermidis.
As you can see there is a lot of white space indicating genes outside a core genome and almost no black (close to 100% match).
This could be due to:
1) Misidentified isolates being called S. epidermidis by the authors of the sequence
2) Sequencing errors
3) Plasmids being forced into alignments inappropriately
4) There really is this much genetic variation at the species level.
Assuming 4) is true, there are a number of interesting consequential ideas:
a) All previous ideas regarding the concept of clonality need to be completely re-evaluated with all non-genomic previous papers claiming clonality disregarded in this aspect.
b) PCR tests and PCR sequencing tests, MMLVA, MLST of genes like rRNA, cytochrome oxidase and other housekeeping genes can be used to group isolates but these groupings only relate to evolutionary history and say very little about what a bacterial isolate currently is.
c) In terms of pathobiology, the term species is almost meaningless. A single base pair mutation in one regulatory gene can fundamentally change how a isolate interacts with a host and how easily it is triggered to cause disease. Given the huge number of differences between isolates of the same species, it is invalid logic to make any pathobiologic statements or assumptions at the species level.
d) Given the genomic differences at the species level, it is completely invalid logic to expect to make a single vaccine or antimicrobial to protect against an entire species of bacteria that do not burn down the house to keep warm (obligately virulent). At best we could hope to make a vaccine against a single isolate, or tight group of closely related, recently diverged isolates.
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Brian, Your answer echoes something of what is discussed by Nesse and by Williams in the book I mention and some other literature in evolutionary medicine.
The host switching idea is key and the book also discusses the correlation of pathogenicity to the ability of pathogens to spread from one host to another. If transmission is easy, the pathogen can completely exploit the current host and then expect to find another easily. An excellent example is the 1854 London water pump handle and the easy spread of cholera.
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Hi, i'm studying about divergence time estimation in Piscis using Beast. But i'm only a beginner, so it's too confused.
In my last question, some kind people told me several tips. And i have additional question.
In calibration to divergence time using fossil data, i only know minimum and maximun age of the fossil, but for log-normal distribution, extinction rate (μ) and standard deviation parameter (σ) are necessary.
The problem is that i can't find the way to calculate parameters mentioned above.
Anyone knows the protocol or website about that, please help.
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Hi Yun,
For a standard, fossil-calibrated BEAST analysis you do not need to know the extinction rate. The mu symbol (µ) is probably referring to the mean. If you want to use a lognormal distribution as your calibration prior, you only need know the minimum fossil age, which would be used as an offset. Of course, the maximum age should be included in that distribution. You can use the maximum age to better inform your lognormal distribution prior. For instance, in BEAUti play with the mean and standard deviation options so you can have the 95% HPD between the minimum age and a biologically reasonable value after the maximum age.
In contrast to hard bound distributions (e.g. uniform), soft bound distributions (lognormal) allow you to sample outside those bounds and better measure uncertainty. 
Cheers,
Santiago
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I would like to measure the impact of corporate governance practices impact on risk management.so i have decided to measure the risk by using DOP and DFL. Are these measures okay?
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Our paper shows how to decompose market beta for financial leverage and operating leverage.  The remaining beta is industry beta. 
Dondeti, V. Reddy, Carl B. McGowan, Jr. and Susan E. Moeller.  “Computing Bottom-up Betas for Companies in the Soft Drink Industry,” Journal of Business Case Studies, Fourth Quarter 2014, Volume 10, Number 4, pp. 357-362.
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Methods based on functional decomposition and morphology belong to the so called systematic design methodology. They are widely taught in accademia, but their diffusion in industry has not reached the same success. Some hypothesis have been formulated by literature, but it is still not possible to identify concrete reasons.
What do you think about that?
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Because everyone believes that without these methods, you can still design well. There is no comparison between design following a design method and not following. (How can we vigorously compare?)
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In a case control study, systematic sampling design for case (with disease) and purposive sampling design for control (without disease non -case healthy individual) can both design be used?
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Hi
selection of controls is the most important point in case control studies. 
•The way of control selection determines:  What is estimated (risk ratio, rate ratio, odds ratio) and the validity of estimate.
Three basic tenets of comparability underlie attempts to minimize bias in control
selection. These are the principles of study base, deconfounding, and comparable accuracy.
Comparable accuracy principle. The degree of accuracy in measuring the exposure
of interest for the cases should be equivalent  to the degree of accuracy for the controls, unless the effect of the inaccuracy can be controlled in the analysis.
Study base principle. Cases and controls should be "representative of the same base experience".
Deconfounding principle. Confounding should not be allowed to distort the estimation of effect.
in this case if you have many cases you can select them systematically but it is better you select the new cases. selecting of control is important. you must first identify the source population that cases arise from it. If your study is a population-based case-control study, that uses a primary base. when ascertainment of all cases in a primary base is difficult or impractical, it may be preferable to use a secondary base. The base is defined as the source of the cases, and controls are individuals who would have become study cases if they had developed disease 
during the time of the investigation. For example, in a hospital-based study, the
cases might be all patients diagnosed with the study disease at one hospital; the individuals contributing to the (secondary) base would be all subjects who would be diagnosed at that hospital had they developed the study disease. 
Finally i think purposive sampling without attention to source population of cases can disturb your results.
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What is the raison d'être of uninformative priors? Isn't one of the Bayesian goals that of allowing to systematically incorporate prior information into inference?
Thanks!
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# If we want inference to be driven solely form data, why do we even bother specifying a prior?
Inference neccesarily goes beyond data, and information is a quantity or entity that exists only in the relation of data and a context (what is here the current "state of conviction" [you may call it "konwlege"], the assumed models, and the kown circumstances of the experiment/study/survey/data collection).
So data alone is and cannot not enough or the only thing to make inference. One needs a model and a context to assert the information of the data (relevant to and related to the model and the context). The model can often be described in some formal way, like a statistical model, either being "obviousely reasonable" or derived from "obviousely reasonable" basic assumptions. The likelihood is the a function that relates the data to the model. This still is not enough to make inference. We still need a context to interpret this function (or likelihood ratios, or p-values from likelihood-ratio tests, etc.). An example can demonstrate this:
If I play lotto (the experiment) the event of winning the lottery has a very small probability under the hypothesis (model) that the result was just a wild guess. The probability of winning would get a mconsiderably higher probability if I had psychic powers so that I could foresee the next lotto numbers. Now I perform the experiment and I win. Wow :) The p-value of this result P(win|guessing) is very small. But would I take this result to conclude that I have psychic powers? Certainly not. But this conclusion is not driven by the data but by the context, by what all we know (or belive) about how the world works. In this context the result remains a "lucky" incident, nothing else, because there is no other data that would be simpler/better be explained from such an assumption and there is such a lot of data that is much more likely if we do not assume that I had psychic powers.
This was quite an extreme example, because we are so sure that psychic powers do not exist (what only means that we would need a hell lot of good data obtained from adequate experiments to reconsider its existence). There are other examples where the influence of the prior knowledge (or believe) is not that drastic.
What is the sense of a so called "uninformative prior"?
Priors are essentially arbitrary. There is no law that would prohibit that two people (agents, social groups, scientific communities) have considerably different priors. Several aspects of the priors can be attributed to (or be seen as consequences of) considering particular (prior) nformation. The above example uses an extremely "informative" prior because there is very much experience about people obviousely lacking psychic powers and because we have no idea how we would integrate the existence of psychic powers into the body of our other models. But if we could not agree on how this information is to be weigted, in other words: if we could not agree on a common wager in a bet for/against the existense of psychic powers? A hoped-for solution is to eliminate all the impact of our former experiencees and of the rest of our models, what would lead to a "non-informative prior".
A sensible non-informative prior is the uniform prior, what says that one considered all possible hypotheses as equally likely. It makes sense in a way that it expresses that we don't see any reason to prefer one of the hypotheses over any other (this is related to Laplaces principle of indifference). However, the hypothesis space may be transformed. But a uniform prior in one space is non-uniform in a transformed space. Here Jeffreys proposed priors that are invariant against transformations.*
# Isn't one of the Bayesian goals that of allowing to systematically incorporate prior information into inference?
No, you turned this around a bit. It is not to incorportae prior information into inference, it is to incorparate the current information into our beliefs (or knowledge). So we do have some beliefs before seeing the data, and the data exhibits a momentum to change our beliefs to a state after accounting for the new data. The data does not tell us where we *are*, it just tells us how far we have to move into which direction. You can see data as being a "force" that acts on masses. Defining a force makes sense only in relation to masses. No masses, no forces. The data changes the impulses, but it does not determine what impulse any mass has to have. This depends on the inpulse the mass had before the force was acting on it.
The Bayesian goal is to provide an objective and systematic way to calculate apply the "force" on a given "impulse".
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* you may imagine a binomial experiment to infer a proportion (p). You may argue that the uniform for p in [0;1] is an uninformative prior. You can express the proportion as an odds ratio, or = p/(1-p). The prior chosen above won't be uniform on the scale of the odds ratio. Which one is correct? Jeffrey's prior for the binomial is invariant under this transformation. So giving the posterior obtained via Jeffrey's prior would be convertible between the proportion and the odds ratio. Hence, "non-informative" means that the posterior won't depend on the way the data is interpreted (as proportion or as odds ratio). I personally doubt that there is any "really objective" non-informative prior. That would be like attempt to describe the frequency of a wave without giving any time scale ("fequency" is an entity that exists only in conjunction with "time"; as soon as I remove "time" from my model it makes no sense or it is impossible to talk about "frequency").
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I am seeking quotes definition of the term taxonomy and systematics. I am looking for definition by Myer and Ashlock 1991.
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De Queiroz & Gauthier (1992) distinguish between systematics (the reconstruction or estimation of relationships) and taxonomy (the branch of systematics concerned with the representation of taxa and their relationships in an ordered system).
Others, such as Wheeler (2008), use the term taxonomy in a much broader sence, including for what De Queiroz & Gauthier (1992) would call systematics.
Both viewpoints have merits. Needless to say, taxonomy and systematics are closely connected: you cannot do a meaningful phylogenetic analysis without sorting out the taxon names of your samples/specimens (and vice versa). Still, I like De Queiroz & Gauthier's version because it reflects the dichotomy I see in the literature: papers that are either phylogenetic or taxonomic are more common than papers that are both. Many new phylogenetic studies do not propose taxonomic changes. There might be good reasons for this. Not every systematist is skilled in nomenclature, and sometimes it is better to wait until there are multiple sources of evidence (or multiple papers) before a taxonomic revision is proposed.
These are not the only viewpoints. There is an extensive discussion of the use of these terms in Minelli (1993). (Ironically, ResearchGate classifies user's requests to identify an organism under the heading 'Taxonomy', something most of us would call 'identification', rather than taxonomy per se.)
de Queiroz, K & Gauthier, J 1992. Phylogenetic taxonomy. Annu. Rev. Ecol. Syst. 23: 449-480.
Minelli, A 1993. Biological systematics: the state of the art. Chapman & Hall, London.
Wheeler, QD 2008. Introductory: Toward the New Taxonomy. In: Wheeler, QD (ed). The New Taxonomy. Systematics Association Special Volume Series 76. CRC Press, Boca Raton, pp. 1-17.
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Between CTAB and QIAGEN DNeasy Mini Kit extraction methods which will produce the cleanest and largest amount of DNA for Araliaceae? I am specifically working with leaf material from Polyscias (Tetraplasandra).
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Some more factors are important to answer this question:
is it fresh material, silica dried fresh material or herbarium material?
And what do you want to do with the DNA and in what part are you interested (Chloroplast, Core or Mito ? ).
Cleanest and largest amount is impossible. Usually while "cleaning" DNA you lose a lot, so you have to decide what is more important for you. I like CTAB, you get A LOT more DNA, it is by far cheaper and quality is also quite good. If you are not satisfied with the quality you can perform some purification steps (Precipitation, using kits or whatever)
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I have found only some of the information and - as I am not familiar with the latest taxonomy - these are quite incomprehensible for me.
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Barbara, try GRIN-Taxonomy, they follow APG, and it might provide information that you are looking for. The site is http://www.ars-grin.gov/cgi-bin/npgs/html/splist.pl?12360
Blanca
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What kind of probiotics own the two advantages that both easily colonizes in human gut and is suitable for secreted expression of protein of interest? Is there some systematic literature for reference? Thanks in advance.
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Basically, any probiotic strain isolated from gut microbiota with anti-microbial activity other than AMP production should be a candidate strain for you. We had isolated Lactobacilus helveticus which had potent bacteriocin producing potentials. Identify a probiotic strain which is isolated from gut but at the same time does not produce its own proteins showing anti-microbial proteins.
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Blended Learning is viewed by many experts with different interpretations. When we apply this concept in our class room we need certain specific models which provide systematic procedures or steps to be followed while applying the Blended Learning. Hence, details about  the specific models or strategies to be followed in the Blended Learning would be useful in the real situations. Could you provide details about these Models?
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Blended learning
Blended learning is the combination of traditional face-to-face and technology-mediated instruction encouraging the adoption of platforms such as online learning, mobile technologies and resources that exist in the cloud (Moskal, Dziuban and Hartman, 2013). Blended learning can be adopted also in distance learning and with new information and communication technology its will come ‘the new normal model’ (Norberg, Dziuban and Moskal, 2011). Blended learning has emerged by the development of information and communication technology but very few studies provide educational guidance for institutions (Halverson, Graham, Spring and Drysdale, 2012).
Littlejohn and Pegler (2007) expanded the types of blends to include the ‘space blend’ (face-to-face or online), ‘time blend’ (geography and availability), ‘media blend’ (tools, technologies and resources), and ‘activity blend’ (learning and teaching activities, individual or group). It is essential that a higher education institution defines and supports policies and course design processes that ensure all students access to learning regardless their time of study and geographical location. Many higher education institutions teach in multiple modes which includes on campus, at a distance, online or a blend of a number of modes (Taylor and Newton, 2013).
During the development of blended learning, a spectrum has appeared on course-delivery modalities which ranges from traditional face-to-face teaching to complete online teaching. The first step is the technology enhanced education. Thereafter the blended learning is followed by learning mostly online and finally completely online (Graham, Woodfield and Harrison, 2013). The latter phases of the spectrum are useful in distance learning. There are virtually unlimited possible combinations of face-to-face and technology-mediated education. Each of them are no more or less valid than all the others.
Higher education institutions have started blended learning first in part-time adult education, because students are at work, but the new techniques have become more common also in full-time study. Blended learning has become more popular among young full-time students in Finland, because most of the students work while they study. The experience has shown that the fully online courses are very demanding for many students. Institutions need to solve the technical and pedagogical obstacles in the face-to-face education. The development has led to technology enhanced education, blended learning and learning mostly online. Blended learning presumes the increased capacity of the tutoring of students and electronic libraries (Kettunen, 2007).
According to the research evidence there is no singular best model for blended learning that fits for all. The mode of delivery has a very weak statistical correlation with student success or persistence (Dziuban & Moskal, 2011). Each institution has to select the success factors for the mode of delivery to fit for the purpose and improve them continuously over a span of several years to achieve high quality. It is typical that at the beginning of a course there is face-to-face class to meet and build community, but discussing a complex matter that requires reflection may be better accomplished through an asynchronous Internet discussion forum (Garrison and Kanuka, 2004).
The key issue in the literature on blended learning is the combination of face-to-face and technology-mediated instruction. Even though it has been expanded to geographical, technological and activity dimensions there is still room to add new perspectives to blended learning. Blended learning has a tradition of many decades in Finland. It has evolved to distance learning, which includes essays from literature with practical applications and criticism, service to society, practical training, student exchange, entrepreneurship and development tasks among other things. The integration of research and development into education is a new innovation in higher education and creates capabilities for students to participate in development work after graduation.
Innovation pedagogy
Innovation pedagogy was developed to improve the external impact of the universities of applied sciences and support the regional development (Kettunen, 2011). The institutions respond to the development needs of the enterprises and other organisations in the region. Typically these development needs are multidisciplinary. The universities of applied sciences apply for project funding and integrate the projects into education. Students are offered project studies and they able to learn innovation competencies in the research and development projects (Kettunen, Penttilä and Kairisto-Mertanen, 2013). Innovation competencies are gained in international collaboration and they are valuable to promote entrepreneurship and the export of education (Kantola and Kettunen, 2013).
The positive external impact of the universities of applied sciences is created with incremental or radical innovations (Tidd, Bessant and Pavitt, 2001). Incremental innovations are created by continuous improvement of existing products, services or processes. Radical innovations create new products, services or processes.Successful innovation pedagogy promotes the economic growth, employment and welfare in the regions of the universities of applied sciences. The curriculum is developed to reach out and engage with development activities in the region.
 Individual learning is extended to collaborative and networked learning, which are the modes of delivering education in projects and distance education. The students are offered project studies where learning emerges as learners interact (Vygotsky, 1978). Students work together and develop their problem-solving skills to achieve the practical learning goals (Puntambekar, 2006). Advanced learning takes place in professional education when learners are well-connected to their environment. The networks raise the ability of students and staff to participate and interact when they resolve their shared problems (Cross & Parker, 2014). Networked learning can be supported not only by information and communication technology but also social and international networks.