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Bioinformaticist or Bioinformatician?

Why are there two words for a bioinformatics scientist, bioinformaticist and bioinformatician? Is there a difference between them?

In 1993, when I was hired in my first industry job as what we would now call a bioinformaticist or bioinformatician, I hadn’t heard of either term. When I was asked what I thought my job title should be, I answered computational molecular biologist. I chose that title to recognize my training in molecular biology and my acquired computer skills.

But by 1995, the terms bioinformatics and bioinformaticist had gained widespread recognition. Now, in 2006, it is my impression that the term bioinformatician is more popular than bioinformaticist, and I have bioinformatician on my business card.

The CD-ROM edition of the American Heritage Dictionary, 4th Edition, makes it easy to find all words in the dictionary with the same suffix. For example, I searched the CD-ROM for all words matching the pattern *icist or *ician, where the asterisk is the standard wild card character that matches any number of characters.

The Suffix -ician

In this dictionary, the suffix -ician is defined as “one who practices; a specialist”.

Here are the 45 words that end in -ician that carry this meaning:

  • acoustician
  • aesthetician
  • arithmetician
  • ballistician
  • bariatrician
  • beautician
  • biomathematician
  • clinician
  • cliometrician
  • cosmetician
  • cybernetician
  • diagnostician
  • dialectician
  • dietician
  • econometrician
  • ekistician
  • electrician
  • esthetician
  • ethician
  • geometrician
  • geopolitician
  • geriatrician
  • logician
  • magician
  • mathematician
  • metamathematician
  • metaphysician
  • mortician
  • musician
  • obstetrician
  • optician
  • pediatrician
  • phonetician
  • physician
  • politician
  • psychometrician
  • psychotechnician
  • rhetorician
  • rubrician
  • semiotician
  • statistician
  • tactician
  • technician
  • theoretician
  • zootechnician

Note: The following words, although they end in -ician, don’t carry the meaning of one who is a specialist or expert: academician, Cilician, Galician, Ordovician, patrician, and Phoenician.

The Suffix -icist

The suffix -icist derives from three suffixes, -ic, -s, and -ist. The combined suffix carries the meaning of one who is a specialist or expert in a science or art. Here are the 39 words in the American Heritage Dictionary, 4th Edition, that carry this meaning:

  • aerodynamicist
  • anglicist
  • astrophysicist
  • biblicist
  • bioethicist
  • biophysicist
  • celticist
  • ceramicist
  • classicist
  • cyberneticist
  • cytogeneticist
  • empiricist
  • eroticist
  • ethicist
  • eugenicist
  • gasdynamicist
  • geneticist
  • geophysicist
  • historicist
  • hydrodynamicist
  • hydroponicist
  • immunogeneticist
  • islamicist
  • kineticist
  • lyricist
  • microphysicist
  • mosaicist
  • neoclassicist
  • pheneticist
  • phonemicist
  • phoneticist
  • physicist
  • polemicist
  • psychophysicist
  • publicist
  • romanticist
  • semanticist
  • semiticist
  • slavicist

Note: The following words, although they end in -icist, are derived from words that end in -ism and do not carry the meaning of one who is a specialist or expert: apocalypticist, atlanticist, ecumenicist, organicist, and pacificist.

No Conclusion

The words I identify with in these lists are mathematician and statistician, two -ician words. (I also identify with biologist, chemist, and programmer, but these don’t fall into the two categories I’m examining here.)

Other than that, I use the two words interchangeably. Most people have never heard these words, and it’s a pain to have to spell them out, at which point I just say that I'm a scientist.

New Perl Books

I have added two books on Perl to my want list.

The first is Higher Order Perl: Transforming Programs with Programs, by Mark Jason Dominus. This book, which was published in March, 2005, teaches people like me, who are trained in the procedural paradigm of C-like programming languages, how to use functional programming techniques characteristic of LISP.

The second book is Perl Testing: A Developer’s Notebook, by Ian Langworth and chromatic. This O’Reilly book, published in July, 2005, provides a short guide on how to use Perl’s test suites. I need to learn how to do this for my job.

I am in the middle of reading Intermediate Perl by Randal L. Schwartz, brian d foy, and Tom Phoenix. (I hope to provide a complete review soon.) When I finish, I’ll probably pick up one of these two other Perl books.

I provide brief reviews of other Perl books I have read in the Perl section of my Bioinformatician’s Bookshelf.

Naming Computers for Protein Scientists

Research groups and companies often need to come up with names for many computers. Some systems I have seen are:

I work in a protein-oriented group. In case I have the opportunity of naming computers in my group, I have compiled a list of names of protein scientists. Each of the researchers in the table below was awarded the Nobel Prize in Chemistry or in Physiology or Medicine for research on proteins. In the table, I give the name of the scientist, the name of the prize, the year the prize was awarded, and the brief description of the research that was being recognized by the prize.

Scientist Prize Year Awarded For
Agre Chemistry 2003 “the discovery of water channels” in cell membranes
Anfinsen Chemistry 1972 “work on ribonuclease, especially concerning the connection between the amino acid sequence and the biologically active confirmation”
Arber Physiology or Medicine 1978 (with Nathans and Smith) “the discovery of restriction enzymes and their application to problems of molecular genetics”
Blobel Physiology or Medicine 1999 “the discovery that proteins have intrinsic signals that govern their transport and localization in the cell”
Boyer Chemistry 1997 (with Walker) “the elucidation of the enzymatic mechanism underlying the synthesis of adenosine triphosphate (ATP)”
Deisenhofer Chemistry 1988 (with Huber and Michel) “the determination of the three-dimensional structure of a photosynthetic reaction center”
Edelman Physiology or Medicine 1972 (with Porter) “their discoveries concerning the chemical structure of antibodies”
Fenn Chemistry 2002 (with Tanaka) “their development of soft desorption ionisation methods for mass spectrometric analyses of biological macromolecules”
Fischer Physiology or Medicine 1992 (with Krebs) “their discoveries concerning reversible protein phosphorylation as a biological regulatory mechanism”
Gilman Physiology or Medicine 1988 (with Rodbell) “their discovery of G-proteins and the role of these proteins in signal transduction in cells”
Guillemin Physiology or Medicine 1977 (with Schally) “their discoveries concerning the peptide hormone production of the brain”
Huber Chemistry 1988 (with Deisenhofer and Michel) “the determination of the three-dimensional structure of a photosynthetic reaction center”
Kendrew Chemistry 1962 (with Perutz) “their studies of the structures of globular proteins”
Kornberg Physiology or Medicine 1959 (with Ochoa) “their discovery of the mechanisms in the biological synthesis of ribonucleic acid and deoxyribonucleic acid”
Krebs Physiology or Medicine 1992 (with Fischer) “their discoveries concerning reversible protein phosphorylation as a biological regulatory mechanism”
MacKinnon Chemistry 2003 “structural and mechanistic studies of ion channels” in cell membranes
Merrifield Chemistry 1984 “his development of methodology for chemical synthesis on a solid matrix”
Michel Chemistry 1988 (with Deisenhofer and Huber) “the determination of the three-dimensional structure of a photosynthetic reaction center”
Moore Chemistry 1972 (with Stein) “contribution to the understanding of the connection between chemical structure and catalytic activity of the active centre of the ribonuclease molecule”
Nathans Physiology or Medicine 1978 (with Arber and Smith) “the discovery of restriction enzymes and their application to problems of molecular genetics”
Ochoa Physiology or Medicine 1959 (with Kornberg) “their discovery of the mechanisms in the biological synthesis of ribonucleic acid and deoxyribonucleic acid”
Pauling Chemistry 1954 “research into the nature of the chemical bond and its application to the elucidation of the structure of complex substances”
Perutz Chemistry 1962 (with Kendrew) “their studies of the structures of globular proteins”
Porter Physiology or Medicine 1972 (with Edelman) “their discoveries concerning the chemical structure of antibodies”
Prusiner Physiology or Medicine 1997 “his discovery of prions—a new biological principle of infection”
Rodbell Physiology or Medicine 1988 (with Gilman) “their discovery of G-proteins and the role of these proteins in signal transduction in cells”
Schally Physiology or Medicine 1977 (with Guillemen) “their discoveries concerning the peptide hormone production of the brain”
Skou Chemistry 1997 “the first discovery of an ion-transporting enzyme, Na+, K+-ATPase”
Smith Physiology or Medicine 1978 (with Arber and Nathans) “the discovery of restriction enzymes and their application to problems of molecular genetics”
Stein Chemistry 1972 (with Moore) “contribution to the understanding of the connection between chemical structure and catalytic activity of the active centre of the ribonuclease molecule”
Tanaka Chemistry 2002 (with Fenn) “their development of soft desorption ionisation methods for mass spectrometric analyses of biological macromolecules”
Theorell Physiology or Medicine 1955 “discoveries concerning the nature and mode of action of oxidation enzymes”
Tiselius Chemistry 1948 “his research on electrophoresis and adsorption analysis, especially for his discoveries concerning the complex nature of the serum proteins”
Walker Chemistry 1997 (with Boyer) “the elucidation of the enzymatic mechanism underlying the synthesis of adenosine triphosphate (ATP)”
Wüthrich Chemistry 2002 “his development of nuclear magnetic resonance spectroscopy for determining the three-dimensional structure of biological macromolecules in solution”
Yalow Physiology or Medicine 1977 “[her] development of radioimmunoassays of peptide hormones”

Better Perl CGI

I have begun a quest to learn a better way to carry out Perl CGI programming. This weekend I began exploring the CGI::Application Perl module, written by Mark Stosberg. I haven’t actually started using it yet, but I’ve been doing a lot of background reading.

Here are some useful links for further reading:

Another module that is useful for managing Perl CGI is HTML::Template. Special hooks are available in CGI::Application to use HTML::Template. For more information, see:

An alternative to CGI::Application may be CGI::Prototype by Randal L. Schwartz. A couple of links for further reading are:

A new alternative may be Class::CGI by Curtis “Ovid” Poe. For more information see:

Single Letter Codes

Today at work the following question came up:

What letters are valid in the single letter amino acid code but do not coincide with letters for bases in DNA and mRNA, including ambiguous bases? The context of this question is differentiating between peptide sequences and nucleotide sequences.

I know the single letter amino acid code by heart. I know most of the single-letter base code, but I always get tripped up by which bases are represented by K and M. Here is the table of letters and their meanings:

Letter Amino Acid Base
A Alanine A
B C or G or T (not A)
C Cysteine C
D Aspartate A or G or T (not C)
E Glutamate
F Phenylalanine
G Glycine G
H Histidine A or C or T (not G)
I Isoleucine
J
K Lysine G or T (Keto)
L Leucine
M Methionine A or C (aMino)
N Asparagine A or C or G or T (aNy)
O
P Proline
Q Glutamine
R Arginine A or G (puRine)
S Serine C or G (Strong base-pairing)
T Threonine T
U Selenocysteine U
V Valine A or C or G (not T)
W Tryptophan A or T (Weak base-pairing)
X
Y Tyrosine C or T (pYrimidine)
Z

Examination of this table reveals that the answer to the question is E, F, I, L, P, and Q.

This might be a fun question to use when interviewing a job candidate for a bioinformatics position.

Pod::Usage

I applied for a job that required experience in object-oriented Perl. During the interviews, I was given an oral examination on Perl. One of the questions I couldn’t answer was, “Identify Pod::Usage”.

The correct answer is that Pod::Usage is a Perl module that allows the programmer to use POD (Plain Old Documentation) for creating a usage message when the user doesn’t supply the desired arguments to a script.

I worked out a complete example of the use of Pod::Usage, which I added to my pages on intermediate Perl.

Smooth Scatter Plots

On March 24, 2006, Gregor Gorjanc contributed an example of how to use the smoothScatter() function from the Bioconductor geneplotter package. The blog entry provides links to other resources for plotting large data sets.

This inspired me to add four examples of smooth scatter plots to my collection of R scripts.