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General Procedures

By: K. Gajewski

Introduction

The LPC consists of a number of laboratories. Some procedures need to be done in the Department labs as well. This is a list of the labs and the work that should be done in each.

  • Main lab (004): Houses the computers, reference material and collections, and microscopes. All computer work is done here, and any microscope work requiring the normal microscope.
  • Tree-ring / macrofossil lab (0011): For tree-ring and/or varve measurements (obviously) and macrofossil picking and identification requiring the use of the dissecting scope.
  • Refrigerator room (0012): Sample storage only.
  • X-ray Lab (0013): This lab is to be used exclusively for x-ray analysis of cores. Access is restricted.
  • Core Processing lab (003A): For the subsampling, photographing and basic description of sediment cores, including magnetic susceptibility, weighing of samples, etc.
  • For pollen processing use the Department lab (003C).
  • For weight loss on ignition or procedures requiring the high-temperature furnace, use the Department lab 003B.
  • For "dirty" work such as sieving dry sediment, use Department lab 005.
  • The LPC is a research lab for the use of faculty and graduate students, and occasionally undergraduate students working for faculty research projects. It is NOT to be used for graduate course work, or for undergraduate labs.
  • I have placed many of my personal books in the lab. You are free to use them in place, but they should never leave the lab.
  • As this lab is funded by my NSERC grants, work done in this lab should acknowledge this. In any publications, please note these grants in the acknowledgement section. I can tell you how it should be done. It would be nice if copies of all theses and publications are left in the lab for future students.

Main lab (004) procedures

  • This is a dry lab. There should be no chemicals and no water in the lab.
  • There are occasional exceptions to the above, for example, when picking macrofossils from wet sediment. In this case, the basic sieving should be done in the wet lab, and only the final steps done in the 004 or 0011. The wet samples should be kept only on the table with the binocular microscope. Watch out for the computers and their cables.
  • Learn the proper operation of any equipment, including computers before touching them. If you have any questions about use or operation of equipment in this lab, or general questions, feel free to see me or J Bjornson.
  • You are responsible for all of your expendables (slides, chemicals, disks, etc). You can arrange this with your advisor.
  • Contrary to the other labs, you do not need a lab coat or goggles. I don't mind coffee, etc., but please be careful with the computers, microscopes and specimens!
  • The WHMIS rules governing laboratory safety are quite strict. J Bjornson is in charge of the labs, and his instructions must be followed.

Computer use

  • The computers in room 004 were purchased with LPC grants, and work for those projects is the priority. Other students who feel they need access must have permission before using them. In any event, all of the software is available on Geolan.
  • In keeping with the University policy on software as well as copyright laws, no software is to be copied (i.e. pirated) under any circumstance. I will cooperate with the authorities to ensure that this is followed.
  • Furthermore, no software, including freeware or shareware, is to be copied to the hard disks without permission, to protect against viruses.
  • Manuals are to be returned on the shelf immediately after use. Please keep the work area neat.
  • These computers are to be used for data analysis associated with research done in the lab only. Class projects should be done in geolan upstairs, and word processing can also be done there if the computers are in heavy use.
  • The UNIX needs to be kept on all of the time. It is not like a PC, which you can turn off (reboot) at any time and begin again. Never turn the UNIX off or unplug it, as this can destroy the operating system.

Microscope use

  • Never put wet mounts on the Leitz microscopes. If you need to look at wet mounts, use a microscope in the teaching lab.
  • Learn the procedure for properly setting up a microscope, called Koehler illumination. This is described in one of the books in the library. You can always ask me or Monique if you are not sure.

Reference collection use

  • The reference collections are the results of thousands of hours of work! Thus, please be careful with the slides. Report any broken slides, so that they can be replaced.
  • Always put the slides back in their proper place immediately after use. Don't mix the pollen research collection with the teaching collection. The slides and specimens are not to leave the room. If you need to consult a slide, bring a teaching microscope into the room. However, get permission from Monique before leaving a microscope in the lab, as they may be needed for classes.
  • You are encouraged to contribute to the reference collection, and help future students. However, all slides must be from properly identified plants. Please see me or Monique to learn the proper procedure.
  • All texts and reprints, including identification keys are not to leave the laboratory. They may only be consulted in the laboratory, and returned to the shelf after each use.

Taxonomy and biological identifications

  • Improperly identified specimens are useless and poor identifications are a continual problem in ecological work. Identification of biological specimens is never easy. It can take years to learn the identification of any particular group, and many more to become an expert. And, there is no shortcut.
  • It is important to realize that proper identification means that you have considered all of the possibilities, and the specimen can only be the species (or genus, or family, etc) that you have named it. Putting the name of a species on a specimen means that you have considered all of the species in the genus, and only the species you assign fits the characters you observe on the specimen. Similarly for a genus name, etc.
  • Be careful of a problem I have observed with many students. Frequently students will use a picture book, find the picture that most closely resembles the specimen, and assign that name. This is simply incorrect. Proper identification can only be made after considerable study of the group of organisms. It is possible that there are closely related species that are not in the picture book. The differences may be subtle, and indeed, not apparent except under the microscope. Sometimes, the characters you need are not on your specimen, and you cannot identify it. Finally, there is considerable diversity in some taxa, and closely related species may resemble each other in many aspects. Thus, you need to consider all of the possible taxa that your specimen could be - and not only the most common.
  • Another mistake students frequently make is a shortcut that makes for poor science. Say you want to work with pollen, and your site is in the Yukon. It is not enough to learn the pollen from the Yukon, and then identify the grains on your sediment slides. Rather, you should learn pollen identification first, then the local flora, and then begin to work on your slides. Of course, you need to be reasonable. You cannot learn the world pollen flora. No one knows it. But, you need to be a competent palynologist, not a palynologist of the Yukon pollen flora. Organism identification is made by the characters of the specimen, not by range maps or habitat descriptions.
  • To properly identify specimens, you need to use the proper literature - floras, keys, etc. Sometimes, the original literature needs to be consulted. Biological identification comes with experience. The more time you put into it, the better you will be. When you start, plan on spending several hours a day - every day - to learn the group of organisms you will be working with. This is very important, and taxonomy must be taken seriously. You may be called upon to justify your identifications, by experts of the particular group. If this is not clear, please discuss this with me.
  • Putting a name on a specimen is only the first step. Next you need to understand what the organism is: its ecology, its physiology. Read, observe, study.

Lab techniques and procedures

  • Many aspects of science are done using standard lab procedures. The reason for this is to make data comparable between studies. For example, in grain size analysis, the samples are sieved through standard sized screens, using a standardized shaking (the ro-tap) for standard amounts of time. If you deviate from these, you have just introduced another source of variation that you need to consider in your interpretation. Usually, standard procedures are designed to optimize data precision and accuracy within a reasonable time and cost.
  • In other cases, the standard procedure is simple necessary. Water samples need to be kept cool and analyzed immediately to prevent diffusion of gases and biological activity from perhaps changing the chemistry of your water. Pollen grains must be treated by acetolysis, since all the reference books are based on acetolysis-treated material. So, read to find out what are the standard procedures for your analyses.
  • We are preparing sheets explaining standard lab techniques commonly used in physical geography investigations. Ask if these are available for your project. We can also point you to texts which contain descriptions of the methods.
  • On the other hand, part of research is finding methods and techniques for doing work more efficiently, or finding new information in your data. You should always be alert to new ways of analyzing your data. Frequently, new methods come when people read outside of their own field of expertise. But you need to determine how the novelty affects the comparison of your data with the old data.
  • Use of a good sampling scheme ensures you have a representative sample of your population. A good experimental design can help you efficiently find interactions as well as main effects. Exploratory data analysis can help you separate signal from noise, and many statistical methods will suggest relationships in your data. (Of course, it takes a physical understanding to interpret these results.). All of these can be misused but a knowledge of statistics is an essential part of a scientist's training.
  • We have a lot of software available for statistical analysis of your data. Many simple graphical methods can be quite effective, and we are well equipped for sophisticated analyses as well. However, your whole project should be planned with the statistical approach in mind.

Data

  • This section is very important, so please read carefully. Data is the basis of science, and there is a strict protocol.
  • Students working on theses, or working on a research project, must maintain laboratory notebooks. All observations and data should be recorded in these notebooks, as these are permanent records of how the data was collected. These should be kept in ink, all pages dated and numbered. Number the pages immediately after buying it, if it is not already numbered. Lack of information in the notebooks is considered to mean the work was not done.
  • Under some circumstances, data can be collected in loose-leaf form. For example, by tradition, pollen data are noted on count sheets which are kept in 3-ring notebooks.
  • Lab notebooks are kept in the lab, or in your office. Note that while lab notebooks are your property, you are obliged to produce them when requested. This is one of the bases of scientific practice. Thus, they should be neat. When you leave after finishing your thesis, I ask that you leave a photocopy of your notebook in the lab.
  • Practically, you are doing yourself a favor by keeping good notes. You will refer to old notebooks years after the work was done.
  • I don't want to overdramitise it, but these notebooks are important documents. In one recent case from the States, a scientist accused of fabricating data had her notebook taken by the FBI, who analyzed the ink and writing to determine if it was written on the date stated and if the work claimed to have been done really was. Discrepancies between published results and the notebooks were discussed in court. The poor condition of her notebooks contributed to her losing her job. (By the way, her supervisor, who has a Nobel Prize, didn't lose his job, although he was co-author of the paper in question.)
  • Obviously, if you don't have a notebook, or if it is incomplete, this puts doubt on your work. Notes should be written directly into the notebook, and not copied from scraps of paper later. If you are not sure how to keep a notebook, ask!
  • All of the above is true of fieldbooks as well. Standard field books, especially the "write in the rain" variety are the best. Use a waterproof ink. Pencil can be too easily smeared. Some people use drawing pens - that you have from your cartography class - but these are hard to keep clean. The advantage is that the drawings are sharp and clear, and the ink is waterproof.
  • Documentation of computer projects is different, since you will have intermediate files and programs which you don't need to keep. But it is important that you have documentation, of data and programs for anything that you publish.
  • The tendency today is to contribute all data to databanks upon publication of the results. This is, after all, the basis of the scientific method. This data is then available to the scientific community for comparison with new data, etc. This lab is committed to this international effort, and all data collected here must be contributed to the NAPD or appropriate group upon completion of your thesis.
  • The converse is true. You have access to a lot of data that may be of interest. We have many databanks of environmental data available for research projects in the lab, and much more is available on the internet. Use it!
  • Photocopies (or the originals, if your prefer) of all count sheets will be left in the lab upon the termination of the study. Photocopies of the lab notebooks or field books may also be requested. Finally, digital copies of all data should be left in the lab.

 

 

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