Stein Gives Bioinformatics Ten Years to Live
by Daniel H. Steinberg02/05/2003
Lincoln Stein's keynote at the O'Reilly Bioinformatics Technology Conference was provocatively titled "Bioinformatics: Gone in 2012." Despite the title, Stein is optimistic about the future for people doing bioinformatics. But he explained that "the field of bioinformatics will be gone by 2012. The field will be doing the same thing but it won't be considered a field." His address looked at what bioinformatics is and what its future is likely to be in the context of other scientific disciplines. He also looked at career prospects for people doing bioinformatics and provided advice for those looking to enter the field.
What Is Bioinformatics: Take One
Stein, of the Cold Spring Harbor Laboratory, began his keynote by examining what is meant by bioinformatics. In the past such a talk would begin with a definition displayed from an authoritative dictionary. The modern approach is to appeal to an FAQ from an authoritative web site. Take a look at the FAQ at bioinformatics.org and you'll find several definitions. Stein summarized Fedj Tekaia of the Institut Pasteur--that bioinformatics is DNA and protein analysis. Stein also summarized Richard Durbin of the Sanger Institute--that bioinformatics is managing data sets.
Stein's first pass at a definition of bioinformatics is that it is "Biologists using computers or the other way around." He followed by observing that whatever it is, it's growing. He showed the results of performing searches in published papers of the last 20 years for keywords in titles of abstracts. As a baseline, over the last two decades the use of "cell" has roughly doubled while the use of "genome" has gone up by a factor of 10 from 1,000 papers per year to 10,000 papers per year. There were essentially no occurrences of "bioinformatics" before 1992. Since then it has grown to three orders of magnitude up to its current rate of 1,000 papers per year.
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O'Reilly Bioinformatics Technology Conference Coverage |
Is Bioinformatics Really a Field?
The field has meetings, journals, and books. The problem, according to Stein, is that it is a tool and not a scientific discipline. Tools get absorbed into the greater disciplines. There are examples of disciplines defined by a problem domain contrasted with services defined by tools.
Robust scientific disciplines are often defined by a problem domain. For example, a development biologist studies the development of multicellular organisms using what ever tools are at hand. They aren't defined by the tools they use. A pharmacologist studies the interactions of chemicals with physiological properties. Similarly, physicists aren't defined by their tools; they study the nature of matter and energy.
On the other hand, services are defined by tools and they are often time-limited. For example, a microscopist knows how to use microscopes. Now that a microscope is a ubiquitous tool you won't find many specialists in this area. While a pharmacologist has a problem domain, a pharmacist knows how to compound medicines and fill out regulatory paperwork. There are fields that cross over. Stein offered molecular biology as an example of a scientific discipline that has transitioned to a service.
What Is Bioinformatics: Take Two
One of Stein's tests for a discipline is the "Department Of" test. Take your favorite field or service and prepend it with your favorite institution's name, followed by "Department of". For example, he is quite happy with the phrase "the Harvard Department of Genetics." On the other hand, a "Department of Microscopy" seems to him to fit better at an Institute of Technology. He said that for him, a Department of Bioinformatics has the same feel and he doesn't predict the establishment of bioinformatics departments.
Stein returned to the question, what is bioinformatics? In light of his thoughts on services defined by tools and disciplines defined by problem, his answer was simple. Bioinformatics is just one way of studying biology. Whether you think of bioinformatics as High Throughput Biology, Integrative Biology, or Large Data Set Biology, fundamentally Stein argues that bioinformatics is biology.
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Later an audience member asked Stein, "Is it strange when biologists never touch goosh: body parts, liquids.... Steins answer was, "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."
Stein answered another question on whether biologists should be required to take introductory programming classes by saying, "Yes, the computer has become a central tool for biology like the microscope or the centrifuge. Being able to produce your own software for data analysis should be part of the undergraduate and graduate curriculum. In answer to a related question about computational biology, Stein answered that "it is algorithm development. It is a specialized discipline. I think it's a branch of CS."
How Do You Make It in Bioinformatics?
Two years ago there was a huge bubble in bioinformatics with students with BA's in biology who knew a little Perl or Java, or CS people with some biology getting offers for $50,000 to $60,000 per year for entry-level positions from pharmaceuticals and bio tech. More recently, the market has settled down. The 2002 New Scientist salary survey reports the median income for academic positions in bioinformatics is $75,000. This is comparable to the numbers for clinical biologists and slightly better than the numbers for cell biologists.
Stein has some simple advice for how you make it in bioinformatics:
- Learn biology. Investigate the problem domain for bioinformatics.
- Pick a problem that interests you. Don't just follow where you think the hot topic is or what seems to be an easy problem. Consider what you are willing to spend the next decade or two or the rest of your life working on.
- Know your tools. Don't treat your tools as black boxes. Understand how they work and what their limitations are. With a microscope you don't need to know optics, but you should know something about light paths, magnification, and resolution. Don't be afraid to use non-computer tools. Don't find the problems that fit your tools.
- Don't be ghettoized. If you expect to be a scientist and to be doing research then don't come in just to perform services to apply your tools to other people's problems. If you want to write software and provide a service, that's great but do so deliberately.
- Do it because you love it.
After taking time to look back at his own career, Stein advised the audience that "there is an event where you find your true avocation. It's easy to find yourself going down the wrong path. There's no shame in turning back." But, Stein said, when it comes to bioinformatics, "It's the biology stupid".
Daniel H. Steinberg is the editor for the new series of Mac Developer titles for the Pragmatic Programmers. He writes feature articles for Apple's ADC web site and is a regular contributor to Mac Devcenter. He has presented at Apple's Worldwide Developer Conference, MacWorld, MacHack and other Mac developer conferences.
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Showing messages 1 through 10 of 10.
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Bzzz! Wrong....
2003-03-13 21:46:57 anonymous2 [View]
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so nice you posted twice?
2003-03-14 04:20:22 Daniel H. Steinberg |
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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
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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
- 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
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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
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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
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Bzzzt! Wrong...
2003-03-13 22:09:28 anonymous2 [View]
A few critiques...
1. It's "Ernst Mayr" _not_ "Ernest Mayer." If you're going to talk about one of the major figures of the Darwinian synthesis at least get the frickin' names right....
2. Mayr spent many years studying birds in the Pacific (mostly Papua New Guinea if I remember correctly). The assertion that he sat "in his office and look[sic] at other people's data and develop theories of selection" is totally bogus. This is symptomatic of not knowing the literature and the history of the field, and people who make such statements come off looking foolish. Given that he's now almost 100 years old, I think we can forgive Mayr for "sitting in his office" as of late....
3. Otherwise I generally agree with Stein's comments about bioinformatics; the tools and approaches will simply be absorbed into the field of biology. Like any technologically driven advances the novelty will wear off. Twenty years on nobody feels the need to explain how PCR works. There's been lots of stuff published in bioinformatics/genomics recently that is completely and absolutely derivative, and should really end up in 2nd or 3rd tier journals. Simply because it has the shine of "genomics" about it, it gets published in fairly high profile pubs. Those days are numbered. Get in on it while you can... ;)
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Bzzzt! Wrong...
2003-03-14 04:16:15 Daniel H. Steinberg |
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Dear Anonymous poster,
I apologize for the first point. That is my mistake and not the speaker's. I am not a biologist and, although I ran the article by several scientists before publishing, the mistake is mine. The hostility in your anonymous is understandable.
The second point is the speaker's and I'm not sure that you and he disagree. Whether or not Mayr spent many years in the field, the speakers point was that much of his contribution was due to his analysis of data collected by others. He was making a positive point about Mayr and pointing out that biology is not limited to the laboratory or field collection of data. Mayr doesn't have to be out in the field during his 90's to continue to contribute to his field.
Daniel
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50-60k is an average starting salary
2003-04-30 08:53:35 anonymous2 [View]
for CS people anyway.
The real question is: 10 years from now who which title will be in more demand in academia and industry - computer science phd or bioinformatics phd? -
50-60k is an average starting salary
2004-01-13 10:50:18 anonymous2 [View]
I was making $130K in bioinformatics until last year. I'm making a little more now doing XML/database consulting. I hope to go back. It is simply more challenging than anything else at this time.
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Bioinformatics - 10 year life remaining
2003-12-30 17:28:00 anonymous2 [View]
I agree with Dr. Stein, although 10 years seems a bit long. I have watched as automotive M-CAD and E-CAD development have been exorcised from the car industry over the last 15 years. The car companies turned against their own children (human and software) with fury and hate. Of course, they are perfectly happy to continue using the software long after the developers have been 'offed.' The basic process involves using public derison against both the developers and the tools they made. COTs or other great commercial hopes are held out as the answer. When these prove inadequate or late, the old software is used in the extended interim.
I have managed to survive by staying ahead of the curve. Unfortunatly, the curve always dies in frustration and hate. Bioinformatics will be reduced to just another service, probably done offshore by transnationals who will charge a s mall 'on demand' fee for the requests made by service consumers. Except for the top people, the rest of the Bioinformatics community might as well get ready to train their replacement sooner rather than later.
Yes, I do plan to learn Bioinformatics at the graduate level starting this winter, but I have no illusions about a sustainable future for that field in this country (USA.) We will simply have the bottom cut out from under us. Do it for love and plan to kiss it goodbye really soon.
Regards,
Steve Lenk
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...