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Bioinformatics in The Economist
Erich Schwarz writes "Bioinformatics has gone from being an esoteric sub-field to being a business. The Economist gives a useful overview, while warning 'Bioinformatics is not for the faint of heart...'"
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If I had to do it again, I'd definitely choose biology or bioengineering or something related.
It seems as most everything in computer has "been done", and biology/chemisty/biochemical engineering seems to be where all the fun & excitement is these days.
Anyone else agree? Just curious.
Is it really what we want/need as humans? I'm not sure. But I for one won't wager a guess until there's more research done in the area, so I say let's explore it more before we defame it conclusively or support it as a technological breakthrough.
Some other recent news items:
... Development Agency (NABDA) and the United Nations Education Scientific and Cultural ...
Nabda, Unesco Collaborate in Bioinformatics Training
AllAfrica.com,Africa-05 Dec 2002
Organisation (UNESCO), penultimate Tuesday held a two-day Bioinformatics
Bioinformatics ahead for Danville
... Developing these plants will involve both horticulture and bioinformatics and will ...
Danville Register and Bee,VA-30 Nov 2002
be one major focus of Danville's Institute for Advanced Learning and Research
The race to computerise biology ...
Economist (subscription),UK-12 Dec 2002
Welcome to the world of bioinformatics--a branch of computing concerned
with the acquisition, storage and analysis of biological data.
Observing Proteins And Cells In The Wild: Quantum Dots May ...
... Today it is internationally renowned for research and graduate education ...
Science Daily-13 Dec 2002
in the biomedical sciences, chemistry, bioinformatics and physics.
Proteomics will be THE next medical frontier. Maybe we will finally understand how proteins work and consequently, how living things are built. That will eventually lead to real genetic engineering and maybe an organism could be constructed from scratch.
The biggest trick the devil pulled was letting lawyers become politicians so they can write the laws.
What, so you can represent each possible codon as a single bit? Last I checked, you can represent 64 values with a measly six bits. (2^6 = 64).
...
Run, don't walk to bioinformatics.org and contribute!
The first O'Reilly bioinformatics conference rocked. Shame I wont make the next one in San Diego - I get to go to Adelaide for the ISMB in June instead
I don't read your sig, why do you read mine?
I'm not sure from whence came all your 'hences' but the sixty four combinations of ACTG only translate into 20 (some argue a few more) amino acids and start/stop signals. The system is highly redundant to lessen the impact of single-base polymorphsims (i.e. if a codon is CCA and the second C is copied as an A accidentally the same amino acid still can be produced in the end-result protein chain).
... it's not 64bit computation. It's ~23bit computation ... but all those other buzzwords are fun too. :)
So hence
-j
And then it would proceed to EAT ALL LIVING THINGS before dying and leaving the planet barren, lifeless, and covered with a strange ooze.
...
Yes, it's an important field. It's been an important field for decades. And it's going to continue to make steady progress, not because of, but in spite of the attention and hype, and the stupid patents and opportunism that come along with it.
I'm not dissing the article completely yet (as I haven't finished reading it, and don't know if I'm completely interested), but I find it wonderful how ignorance among press still prevails.
There is no science, (apart from Math itself - which I consider more of an Art) that has mathematical exactness in it. The word science comes from the latin root of scientia, and means knowledge. Sciences are disciplines where as much knowledge about the existing (thus empirical) world is gathered as possible, and models are generated based on this data.
Mathematics on the other hand, derives from Axioms, and Logic. Both of which aren't derived from the empirical world. And I say it's much more akin to Art because it is a skill that you develop to be a mathematician: you forge out of simpleness new more complex theorems. You are 'creating' them... (in science, you are looking for them).
To make a long story short, there is no such thing as a mathematically exact science.
Hmmm. Seems like it would be easier to say that everything which has been done in computer science has 'been done', whereas everything that hasn't been done in computer science, 'hasn't'.
Seriously, though, you may be mis-categorizing your subjects. Look at computers as computational entities, rather than disk drives, monitors, and so forth. In that case, an optical computer or a biocomputer operates on many of the same systems priciple as a 'digital computer', and there is therefore much to be done in the field of computer science.
Absolutely. Optical computing is getting some great advances in Holographic Video at the MIT Spatial Imaging Group. And chemical computing is advancing nicely in Carbohydrate Chips at the University of Chicago.
For my money, I'd bet on optical video cubes, 3D television, and biochips in the future... which are all applications of computer technology. Remember, 'computer' use to refer to the job title of a person.
For my money, I think that the future has got SnowCrash, Cryptonomicon, Neuromancer, Count Zero, Mona Lisa Overdrive, and Johnny Mnemonic written all over it (and maybe a bit of Jurassic Park.
What you can do, however, is apply computer science and engineering skills to biological problems: work as a developer or engineer for a biotech company or lab.
In fact, I know at least one biologist/scientist with a certain company that drives a Ferrari. Additionally, there is some other rather nice hardware in the parking lot whenever I drive by which is well deserved and hard-earned as this company is one of the hotter ones in the biotech industry with more than a little talent there.
Visit Jonesblog and say hello.
"player 4 hit player 1 with 0 stroms"
see, that's because biology is harder than Computer Science -- we're simply not smart enough :)
here's an interesting undergrad project for you -- how many famouse computer scientists in the past 40 years have originally started as mathematicians.
how many as physicists?
here's an interesting undergrad project for you -- how many famouse computer scientists in the past 40 years have originally started as mathematicians.
Actually, here is an interesting bit of information/history on famous mathematicians and computer scientists who have made it big. The interesting thing is that the University of Utah is the nexus that all of these guys came through.
Visit Jonesblog and say hello.
funny though, none of those guys look anything like the 'i dropped out of school and look where i'm now at' type so highly touted in the pre- bubble burst era :)
:)
interesting read nonetheless, thanx
I graduated from Rutgers U. (decent NJ state school) in May 2000 with a bachelor's in biology. Back when I decided to major in bio, I really enjoyed studying the field, and (high school) teachers were telling me that molecular biology was the fastest growing job sector. So by the time senior year came around I began looking for a "real" job. I checked all the papers, company websites, monster, etc. and realized that there really are NO good jobs out there for biologists. There are a few bioinformatics jobs, but guess what, you need a CS degree for them, not biology. I ended up getting a lousy job as a lab technician paying around $14 an hour (which took several months to find, btw, and this was when the economy was booming), and I'm extremely unhappy. I've completely lost any love I had for this field. Say what you want about money not being the most important thing, but when you can't afford to do anything you want, your life gets miserable very fast, I don't care how great your job is. Biology jobs typically have zero mobility and are extremely underpaid. You think there's a flood of people graduating from CS? Biology is far worse. My CS classes have about 20-30 people in them. My bio classes had hundreds.
Just recently I decided to go back to Rutgers for a second bachelor's in computer science. Not only are the job prospects better and higher-paying (even considering the dot-com collapse), I've always enjoyed working with computers and my grades are actually far better (although I was never a bad student). I'm actually having fun in my CS classes, I never had fun in bio. The classes were more like a chore. Another horrible thing about biology is that you really don't learn anything practical in college, you just memorize facts. At least with computer science you learn many useful tools to make you a competant programmer, which is actually a marketable skill. Nothing about biology is marketable. I highly discourage anyone from majoring in Bio unless they seriously, seriously love it and intend to get a PhD and devote their lives to research without regards to trivial things like money and job prospects.
Karma: Excellent (In Soviet Russia, karma pimps YOU)
I kind of hope I don't get modded down for this as I am totally serious: This is one of those posts where I didn't know whether to mod it "Insightful" or "Funny." Perhaps we need the new mod: "Lost"
Sunny
Be my Friend
Bioinformatics is a fun interesting field. I worry however, that it may be a little overhyped. People who are interested in bioinformatics need to realize it is a very (albeit cool) specialized field. There aren't going to be a million more bioinformatics researchers in the world. The demand for these researchers just isn't there (and won't be there in the near future). For example, a search on hotjobs reveals only 51 listings for the keyword bioinformatics and nearly 900 listings for programmer.
That said, bioinformatics is exciting. If a computer savy person is interested in getting into it, they should intern or work for a researcher/professor on a research project. You might be surprised, however, when you find that working as a programmer elsewhere pays 2-4 times more.
-Sean (sdm@stanford.edu)
An interesting overview about CI can be found at Nature.
Still, you need dedication for this job: A Ph.D. in chemistry plus solid computer science knowledge is still the norm. But those few who qualify are really sought after.
Disclosure: I am the Director of Chemoinformatics at start-up ChemCodes (www.chemcodes.com), so I know what I am talking about.
goto www.lanl.gov and click on the 'jobs' tab then the postdoc link.
here is one example:
Summary: Postdoctoral Positions in Protein Bioinformatics and Structural Genomics: The Bioscience Division (B-2 Group) is seeking 2-3 highly motivated researchers for immediate openings to work with our interdisciplinary team of Bioinformatics and Structural Biology. Research activities will focus on the development and application of methods in Functional and Structural Genomics, including: 1) inference of function in proteins based upon structural and sequence information; 2) prediction of protein structure, protein binding, ligands, and active sites using both ab initio approaches and experimental information; 3) identification of signatures of pathenogenosis; 4) annotation and analysis of selected genomes; and 5) creation and curation of annotated protein databases.
Required Skills:Experience in at least 2 of the following areas is required (more than two areas of experience is highly desirable):
- Protein structure modeling or protein-ligand analysis or other related modeling
- Background in molecular biology, or microbial pathogenesis, or related fields
- Experience with the common sequence analysis tools for Blast search, sequence alignment, phylogenetic analysis, etc.
- Drug design, or protein design or protein structure predictions or docking
- Functional annotation of putative genes based on literature analysis
- Curation of biological databases and web programming
Desired Skills:Knowledge of one computer programming language (e.g., Perl, Python, FORTRAN, C++). Use of common molecular graphics tools such as Pymol, Xtal. Research in genomic sequence analysis or protein structure. Familiarity with SQL databases, unix, and XML is useful. Education:A Ph.D completed within the last 5 years or soon to be completed is required. Notes to Applicants:Starting salaries range from $59,300 to $67,300. For further technical information about the position and the project, contact Charlie Strauss at cems@lanl.gov (505-665-5838), or Murray Wolinsky at murray@lanl.gov (505-665-0952).Candidates may be considered for a Director's Fellowship and outstanding candidates may be considered for the prestigious J. Robert Oppenheimer, Richard P. Feynman or Frederick Reines Fellowships. Please see Special Postdoctoral Fellowships for further details.
For general information refer to the Postdoctoral Program page.
Some drink at the fountain of knowledge. Others just gargle.
http://www.ncbi.nlm.nih.gov/
and
http://genome.ucsc.edu/
Interesting you should say that, since the foundation of molecular biology owes a lot to noted physicist Erwin Schrodinger, and his little book, "What Is Life?" Most of his speculations were incorrect- he believed that proteins, not nucleic acids, were the information carriers of the cell, for example, but as is often the case, sometimes asking the right questions can be even more important than finding answers. However, it's more than a case of a genius coming in with a bold new idea- by the late 1940s, molecular biology was an idea whose time had come. If "What is Life?" had been written in say, 1890, it would have probably been quickly forgotten- in order to make molecular biology a reality, a critical mass of organic and physical chemistry knowledge was needed, and a variety of chemical and biological techniques like X-ray diffraction, mass spec, chromatography, and cell fractionation needed to be developed.
In my opinion, the "What Is Life?" of the bioinformatics age is J. Craig Venter's whole genome shotgun sequencing method. Once again, a totally different way of doing things, and once again, from an outsider- not as much from the field of study as from every one else engaged in that field. I've had the honor of meeting Dr. Venter and listening to him lecture- he's staggeringly brilliant. He also may be the most arrogant man I've ever met. (And I've also met Stephen Wolfram.) I think often a maverick or an outsider is needed to shake things up and move things forward- either an ingenue who doesn't know the "conventional wisdom" or the hardnosed type who simply doesn't care what everyone else thinks.
Of course, once again, the new idea would have gone nowhere without thre requisite advances, this time in computing, not just in technology, but in computer science (fast algorithms so very important), and also in the development of the miracle that is the Polymerase Chain Reaction. Oh, and with regard to the title of this thread, noted biochemistry student reverseengineer is decidedly more upbeat about the idea of a bunch of "damn biologists drving Ferraris." He wants a 360 Modena, a red one.
"FDA staff reviewers expressed concern about the number of patients who were left out of the study because they died."
"Imagine being able to create a creature which is basicly a living supercomputer! It will break teh limitations of current cpus"
But can it find Sarah Conner?
I'm not certain I follow the reasoning as to why 64-bit computing is ideal for genomics. I mean, it's generally going to be faster and more efficient than 32-bit computing, but that really has little to do with codons. I don't know why you would need to assign a 64-bit number to an element in a set of 64 elements- as other posters have pointed out, you'd only need a 6-bit set of numbers to label 64 things. Besides, saying there are 64 codons is a tad naive, since it doesn't account for things like post-translational modifications to amino acids and nonstandard tRNA anticodons. I hope no one has tried to study the translation of something like collagen (full of modified amino acid hydroxyproline) thinking that the codons were the last word in the formation of the protein. I don't see why 64 bits is optimal as far as the crunching is concerned- are you saying that a 128-bit computer program would for some reason not be as suitable to the task?
"FDA staff reviewers expressed concern about the number of patients who were left out of the study because they died."
except if you happened to apply a genetic algorithm to a bioinformatics problem
Well, yes. That is actually exactly what I was implying.
I happen to think that the book is quite good, and I have read it, and I do know what it's about. In fact, I took a class in which it was one of my primary reading sources. The class was entitled 'Cultural Evolution and the Dimensions of Globalization'.
Now then, there are many different ways to skin a cat. There are also many different ways to write an algorithm. I am merely saying that this book is a good source for learning more about optimisation problems, and how to code evolution programs, utilizing genetic algorithms. When you finish the book, you will understand that 64bit computing is an ideal (although not necessarily perfect) platform for bioinformatics and genetics work. Yes, I agree that it is not the only platform, but it is an ideal platform because a 'genetic data chromosome' can easily be written for all of the codons utilizing a 64bit vector.
Yes, actually. The point of the reading was to gain a greater understanding of how to optimize traveling salesman problems for distribution of global resources. We weren't just talking about cultural evolution and the dimensions of globalization to make us feel better... Rather, we were going through the mathematics of how to solve the traveling salesman problem and calculate memetic distribution amongst society. Topics included:
evolutionary genetics (genetics, memetics, bioinformatics, change management)
epidemiology (vector theory, networks, viruses, propogation, transmition)
demography (demographics, statistics, data mining, forecasting)
economics (markets, networks, advertising, buy/sell functions)
communications (telcom, network programming, routers, collaboration, push/pull)
science and technology (mainframes, personal computers, networks, design)
history (memory structures, databases, file systems)
political science (US Code, social programming)
Anyhow, those were most of the topics covered. It was a graduate level sequence, and I worked in a network programming laboratory at the National Opinion Research Center while I was taking the course. The other reading for that class I used included Knuth's The Art of Programming, Hull's The Structure of Scientific Revolutions, Plato's Republic, and all of Wimsatt's personal publications.
Oh, and the course was taught by four people: a memetic evolutionist, a linguist, a mathematician, and a computer programmer. We would use an algorithmic template (the genetic algorithm) and create an instance and map that algorithm onto each of the above mentioned problems and discuss the pros/cons regarding implementation. There wasn't much purpose of taking the class if one didn't know how to optimize an algorithm.
The only problem is biology is something everyone wants to do. It's what all the highest rated TV shows are about. The people who do it are celebrities on not just geek websites but real news. You have to spend a long time in school and a lot of money to get an entry level position anywhere in it because all the fellowships are taken by celebrities. By the way, biology is not a good degree to go into bioinformatics. Chemistry is where you should be.