Article:
  Stein Gives Bioinformatics Ten Years to Live
Subject:   Bzzz! Wrong....
Date:   2003-03-13 21:46:57
From:   anonymous2
OK, in part a critique of the article and in part a critique of some of the quotes attributed to Stein...


1. It's "Ernst Mayr" not "Ernest Mayer." If you're going to talk about one of the "big names" in the Darwinian synthesis at least get the frickin' names right.


2. Mayr spent many years working in the Pacific (Papua New Guinea being one of his major field sites) studying birds. In no way is it justifiable to say that he sat "in his office and look at other people's data and develop theories of selection." This is utter bullshit, and reveals the sort of fallacies that get propagated when people don't know the field. Please read the literature before you spout off....


3. Otherwise I agree with Stein's point about bioinformatics simply being absorbed into "biology". This is true of many of the "hot" tools of today, like microarrays. 20 years on, nobody feels the need to explain how PCR works...

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Showing messages 1 through 4 of 4.

  • Daniel H. Steinberg photo so nice you posted twice?
    2003-03-14 04:20:22  Daniel H. Steinberg | O'Reilly AuthorO'Reilly Blogger [View]

    Dear Anonymous poster


    I assume that this is a second posting by the same person. It is again unsigned and more offensive than the first. Your last two sentences in the second point are inappropriate for polite discourse.


    Daniel

    • longevity of bioinformatics
      2004-09-24 05:03:17  wjbug [View]

      Hello All,

      First, let me pass on thanks to O'Reilly for sponsoring this conference and specifically to Mr. Steinberg for passing on his view of Dr. Lincoln Steins presentation.

      I think there's a fairly easy way to decide what tone is appropriate for posting comments to a venue your scientific colleagues are likely to peruse.

      I) Express yourself in a manner commensurate with an editorial comment in a scientific journal - e.g., would you want to be quoted in a primary scientific publication such as 'Nature' and 'Cell' or a scientific news journal such as 'Science News'.

      II) Would you use the same tone were you to have attended the conference and made a similar comment directly to the speaker.

      We must assume the statement you are commenting on was put out there by Dr. Stein himself, rather than being an editorial comment made by the author of this article, as it appears in quotes:


      "No, they're studying life. Biologists like Ernest Mayer can sit in his office and look at other people's data and develop theories of selection. When people ask me, I say I'm a biologist."


      Had the author gone to the web in order to find the correct spelling of Dr. Mayr's name, I expect you'd have been much less likely to adopt such a tone. There are many references to this revered investigator available on-line, including the library of the eminent Museum of Comparative Zoology at Harvard which is named in honor of Ernst Mayr (http://library.mcz.harvard.edu/).

      Having made such a preface, I hope I'm now able to express my own criticism cogently.

      I agree with the general content of this anonymous posters comment. I assume my criticism ought to be addressed to Dr. Stein, as the comment is given as a quote.

      First, it is a bit incendiary to express this observation in such a manner. People familiar with Dr. Mayr's work are likely to have strong feelings about whether they agree or not with his deeply considered theories. Whether they emphatically agree or equally emphatically disagree with Dr. Mayr's theories/observations, the notion a seminal contributer to the field would "...sit in his office and look at other people's data..." is likely not to strike anyone in his field as truly reflecting the nature of Dr. Mayr's contribution even over his post-septuagenarian years.

      There is a significant difference between performing novel experimental field and/or benchtop research and working to cast the body of this research in a coherent theoretical framework. Both means of contributing to a scientific field are absolutely essential to the progress of scientific knowledge. I believe this is essentially the point Dr. Stein was seeking to express in his extemporaneous reply to a question after his talk.

      My bigger concern, however, is with what I assume based on this report is Dr. Stein's general presentment bioinformatics will be absorbed into the various biological fields to which it is relevant. This appears to be based on the argument "bioinformatics" is a tool analogous to a microscopy or PCR. My difficulty with this argument is these latter "tools" are based on specific physical principles which - broadly defined are:

      • microscopy: diffraction, transmission, reflection and/or emission of EMF radiation of various frequencies of to produce description of a material based on its physico-chemical properties
      • PCR: temperature-cycling-induced annealing of polynucleotides leading to the amplification of specific individual nucleotide sequences either for the purpose of detecting or producing said sequences.


      Though both of these techniques have extremely varied means of application, those general physico-chemical principles are in effect in all these situations.

      Bioinformatics can be broadly defined as:
    • bioinformatics: computer-aided organization, manipulation and/or analysis of biological scientific data

      Not only does this definition extend well-beyond the specific application of computational tools to bio-molecular sequences & structures - the application subject to a decade-long, massive proliferation starting in the late 1980s - it is also so general a category as to be nearly unlimited in its applicable problem domain. Whereas technical innovations - and thus novel experimental observations - using microscopy or PCR need to provide a new means to address the aforementioned physico-chemical principles, the properties being exploited in bioinformatics data manipulation appear to be constantly expanding. Witness the proliferation in the past several years of principles culled from the confluence of computational linguistics, artificial intelligence and database research leading to the wide-spread application of knowledge-frameworks, ontologies and controlled-vocabularies as a means to identify and perform correlative analysis on the semantic qualities of biological data.

      I believe this leads to two results:

      • the spread of bioinformatic applications to an ever-increasing collection of computational disciplines;
      • the extended presence of the various "-ics" - genomics, transcriptomics, proteomics, pharmacogenomics, physiomics, behaviomics (http://ihome.cuhk.edu.hk/~b400559/2003j_functa.html), ecolonomics, evolutiomics (sic) - over the coming century. I believe the existence of these technical disciplines will not only continue through the century, they are likely to uniquely inform & rejuvenate various other biological disciplines such as systems biology, multigenic analysis and complex ecological modeling.


      Just my $0.02.

      Thanks again for covering the conference.

      Cheers,
      Bill Bug
      Laboratory of Bioimaging & Anatomical Informatics
      Dept. of Neurobiology & Anatomy
      Drexel University College of Medicine
      www.neuroterrain.org
      William.Bug@drexel.edu
  • longevity of bioinformatics
    2009-09-26 05:59:58  YangHai [View]

    Thank you, Mr. Bug for your insight on this topic. As a prospective graduate student in the field of Bioinformatics, I find your critique to be absolutely necessary for this subject. I came across this topic as I was researching the field of Bioinformatics and was shocked at the title, so I dug in some more. Since this isn't an actual scientific article or journal, I knew not to take it too seriously, as most of these articles are published for shock-value to fit in with the mainstream media of today, since that is the only thing that seems to reach "news", nowadays.

    I have a bachelors degree in biology with a minor in chemistry and have worked in various industries as a Microbiologist, a QC Chemist, a Validation Consultant, and am currently working as an Associate Technologist in a very successful Medical Laboratory. As for my opinion on the field of bioinformatics magically 'disappearing' in 10 years, I believe this is quite a dangerous statement to be making. It was very discouraging for me to see at first, until I read the article and thought about it, rationally. As far as comparing the discipline of bioinformatics to a 'tool' such as a hammer or a microscope, I do not believe this comparison is valid. The credibility may come in the fact that bioinformatics may be diminishing in ONE aspect of the field of genomics - as we have mapped out most of the genomic sequences in humans and many animals. However, mapping out genomic sequences is just the tip of the iceberg in scientific discoveries.

    Bioinformatics will continue to grow as new technologies and research is developed. We cannot assume that we know everything now that we will in the future. That is what the purpose of research and discovery is. Saying that bioinformatics will be gone by 2012 is like saying that no further discoveries will be made in the field of science.

    As we grow more and more technologically developed, the field of bioinformatics will expand to fit these demands. We are relying less and less on paper and more on large databases and softwares that interface with machines. For example, at the company I currently work for, we are using top of the line equipment to do tests in the fields of hematology, microbiology, chemistry, toxicology, and etc. All these machines are interfaced to a computer and all these computers are lined with software that is constantly being updated as new developments are made in the field of informatics/bioinformatics. We use computers now as our 'Quality Control Officers' rather than relying on tedious number crunching of countless data - a computer does this much faster.

    As far as I can see, having worked in the field, and explored the job market in the life science field extensively, there is no shortage of demand for Bioinformatics, in fact it is quite the opposite.


    Thank you,

    Hai Yang
    • longevity of bioinformatics (cont'd)
      2009-09-26 07:55:07  YangHai [View]

      To elaborate, if the synergy between computer science/informatics and biology did not exist, we would never have mapped out the genomic sequence in the time that we did. Just because we have accomplished one task does not mean we should so easily discard the discipline and field that got us there. As I realize this article is a bit out dated and we have all come to realize that Bioinformatics is not going to just disappear. Fields and disciplines like this may lay dormant for a while, but they never truly disappear. It had a fast growth at first due to the tedious nature of its origins, but its potential has just begun to be dived into.

      Since the time this article was written until now, we have seen an increase in the field of Biomedical Engineering as well as many other advances in the life science industry. High-throughput machines are on the rise, and with it comes extensive data to be analyzed. Bioinformatics rises with the call and demand of its parent discipline: Science.

      Hai Yang
      yang.hai82@gmail.com
      Indianapolis, IN