Bioinformatics in The Economist 208
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...'"
What I'd major in (Score:5, Interesting)
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.
Re:What I'd major in (Score:2)
Re:What I'd major in (Score:2, Insightful)
What about quantum computing? Chemical computing? Optical computing?
Viewpoints (Score:5, Interesting)
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 [mit.edu]. And chemical computing is advancing nicely in Carbohydrate Chips at the University of Chicago [uchicago.edu].
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.
Re:Viewpoints (Score:3, Interesting)
Sure, the future has Neuromancer written all over it. But it also has Schismatrix written all over it as well. We're likely to see biological modification (including genetic alteration) in the future. Even if the majority finds gene-tampering taboo, there WILL be groups that will do it.
The truth is, we're likely to see a combination of the two in the future. Yes, we're likely to see a computer-saturated world within the next few years (if you don't consider it computer-saturated right now), but that doesn't mean we won't see designed genetics as well. The two work together. It's not an either/or issue.
Re:Viewpoints (Score:2)
I think computing is going to move in that direction, as well. Libraries are much too complex and interdependent to be understood by the programmers who use them. We are more likely to manipulate large libraries and pre-programmed objects, working in increasingly visual environments with only a few specialists tweaking specific low-level libraries (and those specialists not necessarily understanding each other's work). I think that there already is a sort of nostalgia for the epoch of computing when any dedicated amateur could pretty much comprehend what was going on in their machine.
Re:What I'd major in (Score:3, Interesting)
Whether you look at artificial life, prosthetics, advanced protein sequencers, electronic "noses", even robotic pets, it seems like at some point what we think of as electronics and computers, and what we think of as genetics or biology are all going to be part of a continuum.
I don't think it matters what you majored in--these days you can cross over.
Re:What I'd major in (Score:3, Insightful)
When it comes to bioinformatics, this is certainly true. However, to be successful in bioinformatics, people need a basic knowledge of chemistry, biology, molecular biology, genetics, programming, medicine, comp. sci. and perhaps some library science to be proficient in bioinformatics and this combination can be hard to come by. Additionally, an ability to successfully communicate with folks from all of those disciplines is crucial and can be even harder to come by. For another article on some of these issues in bioinformatics (with an admitted bias towards the Macintosh) read this article [applelust.com] I wrote for Scientia et Macintosh [applelust.com]
Re:What I'd major in (Score:5, Informative)
I guess there'll be a few with outright credentials, some more who are smart enough to wing it while they learn what they're missing, and a lot of people who contribute as part of a team.
If you haven't read Ship of Gold by Gary Kinder, about Tommy Thompson's life and eventual recovery of $1 billion in gold from the deep sea, I strongly recommend it, especially to any scientific or engineering-oriented person. Tommy's story is a case study in how to break new ground, think creatively, and form networks of expertise. It convinced me that credendials, and even past experience, may not be the best indicators of future success.
Re:What I'd major in (Score:2)
Um, sorry, but it's extremely difficult to go anywhere in the sciences without a PhD. I seriously doubt that will change any time soon. The people doing the hiring are biologists, and would not even bother to read the resume of a whiz-kid programmer unless he had some letters after his name.
Re:What I'd major in (Score:3, Interesting)
I know what you're saying, and I basically agree in most cases. However:
Tommy Thompson, through rigorous thinking, relentless networking, holistic design, etc... Achieved a scientific and engineering feat which far outdid the full resources of the US Navy, Woods Hole Oceanographic Institute, and, of course, countless treasure seeking dilettantes, while spending only a few million dollars from individual investors.
He did not have a PhD, but spearheaded and managed a revolutionary project that led him to employ his former superiors at Battelle, a major defense research lab.
When his team finally found the site of the SS Central America and saw her riches via his revolutionary deep water robot (late 80's), he wouldn't touch a coin before completely photographing and videotaping the site to preserve its archaeological integrity. Each coin of the thousands recovered was individually photographed in place and once retrieved by the robot, while some on the team groused at the delay.
It is difficult to convey the holistic nature of his approach in just a few paragraphs. But I believe his example proves my point that in a new field (in his case, deep water exploration and recovery), precise credentials don't matter.
If somebody thinks you can help him win the Nobel Prize, he'll hire you. If you use letters after your name and a resume to convince him of that, fine. If a 30-minute conversation does the trick--hey, that'll work too.
Re:What I'd major in (Score:3, Interesting)
If somebody thinks you can help him win the Nobel Prize, he'll hire you. If you use letters after your name and a resume to convince him of that, fine. If a 30-minute conversation does the trick--hey, that'll work too.
This all sounds great. There are two problems:
1. Bioinformatics is a hot field, but not really a new enough of one to be a true meritocracy the way you describe. It's very important, but there are already many people actively doing research or getting their degrees. You can't just break into the field (unless you already have a scientific reputation). Barring a degree, a lot of publications helps- but that's going to take a while and involve considerable effort.
2. You have to get to the point where you get the 30-minute conversation first. This is harder than it sounds. I was offered only one interview, and landed a job that was aimed at PhDs or really advanced people (I was not even through with college). However, all of the people interviewing me knew my boss personally. So I was aided by my connections, and it took a while to get those. Had circumstances been different, they probably wouldn't have bothered to contact me.
(I ended up not taking the job- it would have forced me to wait much too long to attend grad school, and didn't quite pay enough to make that worthwhile. Though I confess I still wonder if I made a stupid mistake. . . most jobs for people at my level are along the lines of "database jockey" or "web monkey". These people wanted me as a scientist, probably the highest compliment they could have paid me.)
Re:What I'd major in (Score:2)
I work for a genetic research company and was do not have a degree of any sort. I was hired because my past work experience demonstrated I could program. I knew almost nothing about the science, but when a project is assigned to me, a scientist will explain to me the information I need to know. A programmer doesn't need to understand everything about science to program systems to support it just like a game programmer doesn't have to be a pro basketball player to program a sports game. It just takes an open mind, and willingness to listen to what your customers (in this case scientists) need.
Re:What I'd major in (Score:2)
Re:What I'd major in (Score:2)
My copy of America's Lost Treasure is on its way from Amazon. For those who haven't read Ship of Gold, what you will crave more than anything as you read it is pictures.
Apparently, Tommy's coffee table book is a near-perfect complement to Gary Kinder's excellent narrative. I must say, Mr. Kinder is a brilliant writer, however some of the scenes he describes strain even the vivid imagination.
As a person with no imagination at all, I can't wait for the picture book.
Re:What I'd major in (Score:3, Insightful)
Re:What I'd major in (Score:3, Insightful)
I agree, and I'd just go one step further. I don't think computing will ever reach a point of stagnation. Computing is about ideas, and as long as we are human, we'll always have new ideas.
Re:What I'd major in (Score:1, Funny)
Re:What I'd major in (Score:3, Funny)
Re:What I'd major in (Score:2)
That's a good counterpoint, but not a great one.
With movies and television, there are plenty of ideas, but the very limited (and expensive) channels of distribution prevent most of them--especially the experimental ones--from being tried.
In computing, the channels of distribution are much broader and cheaper. For less than a hundred dollars and a few days work, anybody can launch a website. Within a few weeks, it will be in most search engines, and if their information is useful, well constructed, or entertaining, that can leverage them into a whole business.
Or you can develop shareware and put it onto download.com.
Or you can invent a new compression algorithm if you're smart enough.
Or you can work on getting computing resources to the poorest people in the world.
I don't know, it seems to me that computing has a near endless future.
I mean, just think about Linux. You have a worldwide, voluntary community challenging one of the greatest companies in history. That doesn't inspire you?
Re:What I'd major in (Score:2)
the next big thing (speaking from the point of view of someone who has spent the last 7 years in a north american university) is biotechnology...
of course i hope i'm disproved -- i like computers, not counting genes...
Re:What I'd major in (Score:3, Insightful)
The difference in modern computing and modern biochemistry/genetics/developmental biology is that bioenginnering is a good deal behind computing. 50 years ago, we were working on making computers work. We didn't really get to working on all the applications of computers until computers could be personalized and used in the home. Bioengineering is still at the point where it's being explored. It's all being done in labs because there aren't "do it yourself" genetics labs you can put in your home. Eventually there will be, but not right now. Therefore, if you want to fark around with DNA, you need a degree and a job. If you want to fark around with computers, all you need is to teach yourself some languages and get a PC.
It's not that computers aren't as exciting as genetics is right now...there's a lot more you can do with computers than DNA at the moment. However, genetics is more exclusive because it is not as availible to the public.
bad idea (Score:5, Insightful)
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.
Re:What I'd major in (Score:5, Interesting)
A decade of scientific failures is indescribably difficult to explain, but it is ungratifying. I have been taking Linux/SQL classes for the last few years trying to steer into the digital world, and thus mine and slashdot's interests are now intersecting.
Yes, having interesting work can only go so far. You still have Senior management flushing the cool stuff you invent down the toilet or left on the vine to rot. At the end of the day , you still have a pile of bills to pay.
looking for meaningful work in MPLS fleabag-at-covat-dot-net
Re:What I'd major in (Score:4, Interesting)
I couldn't have said it better myself. Here's something to chew on. Do you need a bio degree to do bio-sales, bio-business, bio-programming, etc? Most likely not. Biologists generally know nothing about business, sales, or programming, so they can't get jobs in these fields.
I work as a lab tech and I agree that they are ditch diggers. I actually did go to grad school for a bit, I pretty much hated it. It's very unsatisfying. At least if you program you can design something *useful* that *works* and feel like you've accomplished something. Biologists go months without accomplishing anything, and the work is dirty. Who wants to be in a lab for the rest of their lives? Even the PhD's have it really tough. No one hires PhD's, they're overqualified. Most of them end up working long hours for years as post-docs making $30,000.
Re:What I'd major in (Score:4, Insightful)
Re:What I'd major in (Score:2, Insightful)
Biology is hard because Mother Nature is the most dirty hacker on the planet!
Imagine trying to unpick the code of a programmer who:-does not know how to program, so just randomly diddles with the code (any code, the program, the compiler or the operating system she don't care) and uses whatevers just good enough.
who does not know about documenting, or version control
who's software testing is done by the users
and when she does reuse her code, its sometimes the result of two projects converging on the same solution.
Re:What I'd major in (Score:2)
I guess this is true for a lot of people in Math, Physics and other areas too.
Contrary to what people think, there is little money in pure theoretical CS (in my case, AI) research. The only way to get recognized is to show commercial relevance.
The funny thing is that, publications carry you only so far, unlike some areas like Physics where good publications will keep you alive. I guess the same would be true for Biology too, since like CS it is also more of an application level science. Unfortunate, but inevitable.
Re:What I'd major in (Score:2)
Re:What I'd major in (Score:2)
We hire people with various skills. All people, including the biologist (or bioanalist, people that generate and analyze biological data with the tools we make), require a thorough understanding of *nix.
Computer science skills that we are particulary interested in are string matching, graph theory, statistical algorithms, super computing (software that run with 1000s of threads). This is all in C and C++.
We work with (real) computers from every vendor (IBM, Sun, SGI, Compaq,
All, people that work here are either computer scientist with an interest in biology or the other way around. Bioinformatics is a lot of fun, but the market is difficult right now (still troubled by the internet bubble investment hype - some big, well funded companies went down).
We get about 20 resumes per week, most of them applying for a bioanalist position. We have enough of those. We do not get many serious CS applications (finding people with some experience or specific skills is difficult), but when we do we seriously look at them.
So go ahead and check us out [gene-it.com] (shameless plug).
Re:What I'd major in (Score:2)
For example, doing an MSA on a set of strings is easy enough, and the computation involved in the algorithim to find the best alignment is slightly interesting. But the point of an MSA is not to parse the file, but to gain new knowledge from a bunch of data that was previously meaningless. And when we have thousands upon thousands of genetic sequences from various organisms, comparing them on a genetic level is definitely "new and exciting".
A Simple Example
For those that know that Humans are 98.7% similar in DNA to a chimp, the question is really why are we so physically different. Well, bioinformatics, combined with lab research has provided insight into this.
We now know what makes us fundamentally different from the Chimps is that the SNPs that we have that make us 1.3% different are in key locations such as a genes which plays a role in developmentmental processes (and particullaraly the brain). For additional information on this, see: "Intra- and Interspecific variation in Primate Gene Expression Patterns; Science 4/13/02"
And in the 8/16/02 issue of Science, there was a short snippet on the discovery of a particular gene, FOXP2, that plays a role in speech and jaw development. They discuss that mutations in this gene have varied, and wide effects on the phenotypic expression in the organism. Now, lets apply what we know bioinformatics can apply, by asking the question. "What difference in the FOXP2 gene causes the differences between humans and chimpanzees in speech and jaw development".
There are SNP databases out there that have been constructed by analyzing the various known genetic sequences and if you search that database, you will notice there *is* a SNP in humans that is unique to humans.... now we have a really interesting argument to why humans can talk and other species can't. (http://www.geocities.com/asdut2002/FOXP2.html [geocities.com]
Conclusion
So the bottom line is that yes, bioinformatics allows us to do a lot of string comparisions, but the benefit of those comarisions are the real gem. And without computer scientists to construct algorithims, and IT professionals to develop world class database systems, this information just isn't useful.
yeah, damn biologists driving ferraris! (Score:1, Funny)
reminds of the "I love linux" plate someone had on a lamborghini in the late 90's, which used to be shown off at linux shows and stuff...
some people will always make money off the stuff we give for free (like genes
Re:yeah, damn biologists driving ferraris! (Score:2)
Re:yeah, damn biologists driving ferraris! (Score:2)
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?
Re:yeah, damn biologists driving ferraris! (Score:2)
Actually, here is an interesting bit of information/history [utah.edu] 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.
Re:yeah, damn biologists driving ferraris! (Score:2)
interesting read nonetheless, thanx
Re:yeah, damn biologists driving ferraris! (Score:2, Interesting)
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.
The submitter is correct (Score:5, Interesting)
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]
AllAfrica.com,Africa-05 Dec 2002
Organisation (UNESCO), penultimate Tuesday held a two-day Bioinformatics
Bioinformatics ahead for Danville [registerbee.com]
... 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.com] ...
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 ... [sciencedaily.com]
... Today it is internationally renowned for research and graduate education ...
Science Daily-13 Dec 2002
in the biomedical sciences, chemistry, bioinformatics and physics.
Re: What I'd major in (Score:2, Interesting)
Re: What I'd major in (Score:1, Insightful)
This society that we created forces people into things they don't care about so they can eat.
You happen to like computers and it pays right now. So get off your high horse and consider the point of view of other people.
Re: What I'd major in (Score:2)
I majored in Computer Science because I liked the thoughts and perspective involved in programming, not because I was looking for the next hottest thing.
Wouldn't it be great if you could do both? Wait, you can: a lot of the great bioinformaticians are computer scientists (through fields like machine learning).Re: What I'd major in (Score:1)
E.O. Wilson wrote in his autobiography that he picked ants to study because no one else was studying them -- and he freely concedes that he's probably not as brilliant as some of the other biologists, but he picked a field that was new and exciting and he ended up having a lot more satisfaction as a result because he could make important contributions personally in a field that was still sparsely populated.
Re: What I'd major in (Score:2)
Unless you have a PhD in CS or Bio right now or will be getting one soon, I suspect it will be too late to start in bioinformatics. By the time you are considered qualified enough to get a real job, the market will be saturated.
The future is bpu (Score:1, Interesting)
Imagine being able to create a creature which is basicly a living supercomputer! It will break teh limitations of current cpus
We already created a polio virus from scratch, and we are trying to create a organism from scratch.
(bad joke ahead)
Imagine living beowulf clusters, we could create a cell with cpu like properties, they would reproduce by splitting, and your biocomputers computing capacity would double every few minutes!
Now if each cell could perform 1 megaflop then a petaflop computer would need 1,000,000,000 cells. 2^30 is appox 1,000,000,000. So if it took 10 minutes for cells to split, then a petaflop biocomputer could be grown in about 5 hours!
Re:The future is bpu (Score:2)
Re:The future is bpu (Score:1)
Re:The future is bpu (Score:2)
But can it find Sarah Conner?
Bioinformatics, Genomics, Proteomics (Score:2)
Re:Bioinformatics, Genomics, Proteomics (Score:1)
The big problem is figuring out how proteins fold. Once we know a proteins structure, it's often trivial to figure out how it works(it's simple chemistry and physics from their).
The biggest contribution that proteomics could make would be to solve the protein folding problem.
Re:Bioinformatics, Genomics, Proteomics (Score:3, Informative)
trivial either. Lets assume that both proteins say the same shape. Take one protein
rotate it and move it around the other protein
in all possible positions and orientations the
relavent group action is R(3) tensor O(3), (the group transitions of one body in 3d, times the
group of rotations in 3d:
six dimensions. proteins are big molecules,
for each of the possible orientations and positions you need to calculate the electrical and
pauli forces between each atom on the surfaces of
one protein with those on the the surface of the
other protein to see if the there can be any chemical interaction between the two. This is a
heavy ammount of computation. But its worse than
that one protein can change the shape of another
one making the calculations even more complex.
Proteomics needs the folding problem solved.
Protein Protein interaction solved.
The inverse folding problem solved (for drug/DNA design).
Then DNA-protein interaction, and the interactions
with macro sugar molecules. Once you've done all
that and have it tabulated in vest lookup tables
for common problems
and with computation on demand for rarer problems, then you can simulate a single cell.
Re:Bioinformatics, Genomics, Proteomics (Score:2, Informative)
Re:Bioinformatics, Genomics, Proteomics (Score:2)
Of course, it wasn't created from scratch, but it may be the closest thing yet, and the most fully understood non-viral life form yet (many may have heard):
New Life Form Created [siliconvalley.com]
Bioinformatics runs on Open Source (Score:4, Informative)
Run, don't walk to bioinformatics.org [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
Re:Bioinformatics runs on Open Source (Score:1)
Also, if you look around, there are great bioinformatics jobs that don't require specific experience/education.
I know, I've been working in bioinformatics for the last two years and I only have a major in computer science (actually, I don't, I have my last exam friday :) )
Re:Bioinformatics runs on Open Source (Score:5, Informative)
In case you are wondering, there is a biopython, biojava, biocorba, bioxml, biruby, etc. but perl is really where 90% of bioinformatics is done (simply because, in the end, all it is is text processing)
after overhyping the Internet (Score:2)
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.
Re:after overhyping the Internet (Score:1)
The field is just starting to really contribute to society as a whole, with the first drugs developed using rational drug design being used in medical practice [nih.gov].
Who wants just steady progress? Most people want exponential progress in medicine, and that will only happen if the field grows.
Re:after overhyping the Internet (Score:2)
Rational drug design has been around for a long time, and that is not the "first drug" designed rationally. Of course, decades ago, people couldn't do rational drug design by the kinds of large scale simulations we do today, but the principles of rational drug design were still the same.
Who wants just steady progress? Most people want exponential progress in medicine, and that will only happen if the field grows.
Using the term "exponential" similar to "rapid" generally suggest someone who has no idea about science; a steady 3% annual growth rate is "exponential growth", just like an an annual doubling.
In any case, the problem with the hype and bubble approach is that after a few years of spectacular growth and job opportunities, you get many years of spectacular failure and disappointment.
Re:after overhyping the Internet (Score:3, Interesting)
Actually, bioinformatics is just starting out and the hype has not even begun. Just wait a few years. Additionally, bioinformatics is not decades old. It really started to come together about 15 years ago, and is still an emerging field at the nexus of computer science, chemistry, genetics, physiology, anatomy, pharmacology, epidemiology, medicine, engineering, virology, microbiology, pathology, mathematics, statistics, information management and molecular biology. All of these fields are contributing rapidly exploding amounts of information and making sense of all of this information and communicating the results is what bioinformatics is all about. In fact, because of the advent of bioinformatics, new fields like pharmacogenetics, or the tailoring of drug treatments to specific individuals are being created.
For a number of reasons, the major contributor of information to the field right now is genetics. This is because genetic and protein sequences lend themselves to large-scale analysis in a much easier to encode manner and thus are easier to interpret than other types of data such as tertiary or quaternary protein structure, histology or biochemical pathways. This ease of management is because genetic sequences can be easily represented by letters which represent base pairs, and what one sees when examining a genetic sequence from DNA for example is an endless stream of the letters A, G, C, and T representing adenine, guanine, cytosine, and thiamine, the four nucleotides that make up DNA.
You are probably familiar with the relatively recent announcement of the human genome being sequenced. What has been accomplished here is that all of the A's, T's, G's and C's in the human genome have been placed in roughly the appropriate places by a consortium of both private and public research groups. What all of these base pairs mean is another set of problems that needs to be unraveled. For instance, where do genes begin and end in these sequences of letters? What regions encode proteins and which do not? These are only two of literally millions of questions that can now be asked illustrating that this rough draft is only the beginning and it is only one genome out of many that has been sequenced which will lead to a more complete understanding of organismal biology. And this is just the mammalian stuff. The real money will be on advances made in agribusiness.
Re:after overhyping the Internet (Score:2)
Actually, it's a biology background and a bit of perl. (I personally do the perl part).
Re:after overhyping the Internet (Score:2)
Sure, it is: DNA sequence databases, genetic sequence analysis, simulations of regulatory networks, simulations of biochemical networks, 3D structural analysis of proteins, etc. were already in wide use in the early 1980's, and a lot of that goes back to the 1960's.
You are probably familiar with the relatively recent announcement of the human genome being sequenced.
But you are evidently not familiar with the history of biochemistry or molecular biology. Bioinformatics didn't start with the attempts to sequence of the human genome.
These are only two of literally millions of questions that can now be asked illustrating that this rough draft is only the beginning and it is only one genome out of many that has been sequenced
These are the same questions that people were asking before the sequencing of the human genome, and many people still believe that what the human genome project accomplished was not the most cost effective approach to answering them. And it is not the case anyway that the human genome project has delivered an end-to-end sequence of the human genome.
Re:after overhyping the Internet (Score:2)
Of course they were. However back in the 60's, 70's or 80's or even 90's I could not perform quick sequence searches of various species, get a 3-D appreciation of a particular protein and then design and submit an antibody or drug for that sequence in an afternoon. In order to do this, I need databases that have been populated with information developed over decades and tools to mine those databases. That is some of what bioinformatics is about.
But you are evidently not familiar with the history of biochemistry or molecular biology. Bioinformatics didn't start with the attempts to sequence of the human genome.
A bit snippy are we? Actually, I am quite familliar with the history of biochemistry and molecular biology and I never said that bioinformatics began with sequencing the human genome. Rather I was using it as an example as it was widely publicized and well known. Please re-read my previous comment.
Re:after overhyping the Internet (Score:2)
Since you admit that the technologies and software were already available decades ago, what is your point? Are you saying that bioinformatics is about being able to do something in an afternoon, as opposed to having to run it on a mainframe over a few days?
I never said that bioinformatics began with sequencing the human genome. Rather I was using it as an example as it was widely publicized and well known. Please re-read my previous comment.
You wrote:
A bit snippy are we?
No, not at all. It is simply evident from your post that you are a bit taken with the hype and a bit unfamiliar with the history of molecular biology, even if you talk at length and repeatedly about "T's, G's, C's, and A's".
Re:after overhyping the Internet (Score:2)
Sigh.......No......I did not admit that the software was already available in the 60's, because it was not. Bioinformatics is not about individual technologies such as protein crystalization or running gels or finding and quantifying enzymatic activity. Rather it is the overall integration of the knowledge of the individual technologies, and the management and dissemination of the data. This requires databases and tools with which to mine the data present in databases. Yes, we did have databases decades ago, and yes, there was some analysis of those data. However, large scale integration of many different types of data from many different disciplines and techniques was not accomplished until relatively recently.
No, not at all. It is simply evident from your post that you are a bit taken with the hype and a bit unfamiliar with the history of molecular biology, even if you talk at length and repeatedly about "T's, G's, C's, and A's".
What is exciting is that much of this work can now be accomplished on the desktop and for very little money compared with what was possible only a few years ago. As for your griping about familiarity in molecular biology, my original post was simply to inform the general Slashdot community and not get into a pissing match with you or anyone else with an axe to grind or a thread to troll. As for overall competence in science, I would rather rely on my scientific publications, record of work and reputation with colleagues to demonstrate my knowledge and capability as opposed to taking any more time with you shouting into the wind on Slashdot.
Best,
Re:after overhyping the Internet (Score:2)
Progress in bioinformatics has been steady over decades. Many of the capabilities we have now are based on methods and ideas developed a long time ago, although they have much more impact now with powerful PCs.
What we need is steady, continued public research funding in the application of computers to biological systems. What you advocate, and what follows from hyping up a field, rapid expansion and large new private investments, is destructive in the long run.
Re:after overhyping the Internet (Score:2)
Absolutely.
What you advocate, and what follows from hyping up a field, rapid expansion and large new private investments, is destructive in the long run.
I would agree with you here, but I don't think that public attention to an issue is always necessarily a bad thing. It certainly is bad for the science if the "spin" is put on issues to make them more than the science supports. Additionally, I would agree that hyping of any discipline beyond the public expectations can bring difficulty to any field (the U.S. space program, the Internet, the cardiac transplant field, the whole retinal transplant field right now, etc...et
Re:after overhyping the Internet (Score:2)
Now get to my main point about the Internet being Hyped. Yes it was hyped, but rightly so.
The famous remark by Elison "The Internet changes everything" is truer today than when it was uttered a few year ago.
Go thru what you do on a daily basis and think about how this has been changed over the last few years.
All business communication (Human as well as machine to machine) is transformed. Most retail we do is transformed. Brick and Mortar retailers is relying on Internet to promote deals, We all use Google etc. to look at product information.
Science is changed forever as the Internet is now the premier reference vehichle. If a scientific paper is not available online it might as well not exist.
I could jammer on but the point is that the Hype was justified. The Economic dislocation of whealth behind the Hype was the problem, not the hype per se.
Re:after overhyping the Internet (Score:2)
Molecular biology will profoundly change our lives. Bioinformatics is only one of many tools of molecular biology.
Now get to my main point about the Internet being Hyped. Yes it was hyped, but rightly so. The famous remark by Elison "The Internet changes everything" is truer today than when it was uttered a few year ago.
The Internet did change everything, but, like bioinformatics, it was created quietly in the 1960's and grew steadily for several decades afterwards. The hype and feeding frenzy in the late 1990's hurt the further development of the Internet and thrust us into a recession.
So, optimism about both bioinformatics and the Internet is justified, but what commercial applications need is steady, continued investment, not a huge influx of people and money all at once.
Re:after overhyping the Internet (Score:1)
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.
Historically, it appears that investors (and career planners) are not very good at matching the "ramp-up curve" of new tech. The web and HTTP are changing the way business works, but the pace may be more gradule, and in different ways, than investors anticipated.
Technologies like automobiles and telephony did become big industries, but investors over-guessed the first few years and under-guessed a decade or two down the road.
History suggests a gradual, but substantial ramp up in progress for promising new technologies. I am going to wait for some kind of mini-crash about 5 years from now before I invest in biotech stocks. I suspect that the payoff will be slower than impatient investors want, and then it will be a fad to dump biotech stocks after a big biz magazine has a headline like, "Biotech repeatedly dispoints investors". That is the point to jump in.
But, you never know for sure. Predicting the future is a tough biz. The internet has shown that the proliferation of a given tool does not necessarily guarentee profits. It may become a simple prerequisite for survival rather than a profit machine.
Competent columnists... (Score:2)
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.
Revolution (Score:2)
My $.02 on biological sciences (Score:4, Informative)
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.
Re:My $.02 on biological sciences (Score:3, Interesting)
Now, I'm 3/4 of the way through a CS degree, and enjoying school like I never have before. Sure, part of it is a little more maturity/experience, but I find now that I'm in something that I ENJOY, I couldn't care less if I'm learning about NP-Completeness today, or Java Beans tomorrow. Regardless, I'm about to enter a co-op work term that will pay $18/hr - and this is one hell of a lot above average salary around these parts (think closer to $12), even for people with university degrees (maybe $15 if you're lucky).
Good money, really fun work, this is the life. It's certainly NOT what I experienced in the bio field. Ironically enough though, I'll be graduating with my CS degree just as 'bioinformatics' (they've changed the buzzword for this a few times since I was in high school) is supposed to hit the big time. Would be kinda neat to have that microbio degree be worth somethign after all
Re:My $.02 on biological sciences (Score:2, Insightful)
And the fact that there is a large number of people in Biology classes I would hypothesize is related to the number of people who try to get into Medical School. And veternary school and graduate school in biomedical sciences which is a huge and growing field. Whereas I don't think CS majors have that many options.
I am currently getting a PhD in Pharmacology/Biochemistry but just wanted to offer a counter opinion as someone who LOVED Organic Chemistry and Biochemistry and Cell Biology and Developmental Biology. Biology and Chemistry are absolutely fascinating. If you don't enjoy them, don't major in them...just like if you don't enjoy CS....don't major in it. I think that's a better message to send then "I highly discourage anyone from majoring in Bio".
I assume you didn't get a teaching certificate or take any business classes where you could have easily done hospital finances. Or did you look at Government jobs as an inspector of the numerous things the government regulates. Or look to OSHA or some college/company similar organization for training on safety issues. All can be based on a biology degree. Just a couple counter thoughts from a person who loves biomedical science!
Re:My $.02 on biological sciences (Score:2)
No, the correct advice is this:
Unless you plan on going to graduate school for a long time, do not major in the sciences. Without a PhD you're a peon. There's no respect and little room for advancement. Everyone knows that you were pre-med and got one too many B's to continue.
I've got a BS in Chem and missed a Bio minor by a class or two. I loved organic chem, mollecular bio and all of those classes. When I graduated, I switched to the IT field because it paid twice what most science jobs paid.
Who wants to go through all of the rigor of a science major just to get a job as some government inspector? Sorry, I won't ever suggest that anyone sweat through o-chem to become the OSHA guy. If you truly love the field you won't be satisfied with those kind of jobs anyway. Making sure some binder has all of the MSDS sheets doesn't have anything to do with my love for science.
Here's my warning to all high school kids and undergraduates. You won't hear this advice from the admissions department or your advisors.
Do not major in a science. If you do, you should plan on doing one of two things:
1. Get a MD or PhD
2. Double-major in business, or maybe CS
Stay away from option number 2 unless you specifically want to combine the two fields or option 1 doesn't work out. College is a great time in your life. A science degree will take more of your time than most other disciplines. If you don't plan on reaping the benefits, don't put in the work.
There's something to be said for doing what you love. However, what good is it to study what you love in college if you can't practice it once you're out?
Re:My $.02 on biological sciences (Score:1)
As far as I know there aren't many jobs for PhD's either. I work with someone who has a PhD in Chemistry (ok, it's not bio, but chem's probably a better field than bio), and he's a lab tech like me!! Besides, why the fsck should anyone have to get a PhD just for the chance to make a livable wage in their field? If that's the case, I'd say it's a lousy field.
coin analogy? (Score:1)
The analogy that comes to mind is a coin sorter. Is this an accurate analogy? It also appears that there is not necessarily an existing "slot" for many genes, like what happens if you get a coin from a country that your design did not include. You don't know where it will end up.
Re:coin analogy? (Score:1)
Correct, in which case you won't detect the unknown gene.
However, the chance that an unaccounted for gene will falsely trigger another detector "slot" is VERY unlikely; each detector is exceptionally specific for what it is supposed to detect.
Security (Score:1)
Wow! (Score:1)
... They're not kidding! Even the name is hard to spell!
As a bioinformatics scientist... (Score:3, Insightful)
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)
Don´t forget Chemoinformatics (Score:5, Interesting)
An interesting overview about CI can be found at Nature [nature.com].
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.
revolution in biology (Score:4, Interesting)
i recently finished my Ph.D. in cancer genetics. one interesting thing was that something that might've taken me 1-2 weeks to do previously, was now completed in 20 minutes thanks to bioinformatics.
Also, bioinformatics helped level the playing field for most scientists in comparison to the "big labs" that have the money... with a bit of perl, I could parse gigabyte text databases as easily as the next guy.. (of course, the big labs could hire more programmers). but the point is, I wasn't limited by experimental techniques that I couldn't afford. rather, i was limited by only imagination.
some of the new technologies made possible by the Human Genome Project include genomic, expression, and protein microarrays (among others). imagine a scientist dealing with 4-5 experimental results from say doing a northern blot (i.e. assaying expression of some 4-5 genes). now imagine that by using a microarray, the same scientist can examine the expression of 20-30,000 genes at once. again, here is where bioinformatics helps, and scientists having any bit of CS background (perl, C++, databasing, etc) are already one step ahead of the crowd because you don't need to rely on others (who are already time-limited) or the use of (expensive) commercial software.
regardless, computational biology has always been around, but in recent times the relationship and integration with mainstream biology has become intensified. I remember a talk given by Francis Collins [cnn.com] (Director of the National Human Genome Research Institute, NIH -- ie. the public consortium running the HGP) where he stated that the other science disciplines (physics, chemistry,etc) have had their "coming of age" or "revolution", but now biology is just gearing into the limelight and the discoveries made in the next 10 years and onward will impact on us all tremendously.
my $0.02
Space exploration? Nope. Bioinfo? Sign me up! (Score:2, Interesting)
Did we get any customers within JPL or NASA? A few. But we presented one paper outside of the typical computer and planetary science fields, and suddenly we've got more bioinformatics contracts than we know what to do with.
I have to admit, the money's great, and it feels good helping to combat cancer, yet I sort of miss the stars and planets.
What is NOT bioinformatics. (Score:5, Insightful)
"Bioinformatics is actually a spectrum of technologies, covering such things as computer architecture (eg, workstations, servers, supercomputers and the like), storage and data-management systems, knowledge management and collaboration tools, and the life-science equipment needed to handle biological samples."
Now I personally spend my days developing databases and applications in support of biology and chemistry at a Pharma in Cambridge. I would not, however, consider myself to be in bioinformatics. Our bioinformatics people spend their days sifting through protein sequences and running docking models. They need to know about amino acids, not about fibre channel.
Bioinformatics has nothing to do with infrastructure, with document management, collaboration tools, or storage. That is IT, pure and simple. Anyone claiming otherwise is abusing the term in the hopes of tagging along for the ride.
Re:What is NOT bioinformatics. (Score:2)
In one sense this is true. However bioinformatics is not just about applying existing informatics technology to biology. The demands that are placed on the technology often means that the technology itself needs to be extended to work properly.
So while I do know about proteins, and the various bioinformatics resources that are out there, I also know about knowledge representation technologies. The latter might have use outside of biology, but biology provides much push to apply, use, and extend these technologies.
Phil
Postdocs Jobs in bioinformatics and proteomics (Score:4, Interesting)
goto www.lanl.gov [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 [mailto] (505-665-5838), or Murray Wolinsky at murray@lanl.gov [mailto] (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 [lanl.gov] for further details.
For general information refer to the Postdoctoral Program [lanl.gov] page.
Best sources of bioinfo ... for the curious ... (Score:2, Informative)
http://www.ncbi.nlm.nih.gov/
and
http://genome.ucsc.edu/ [ucsc.edu]
Postdoc required (Score:2)
Re:Bioengineering (Score:2)
Re:Bioengineering (Score:1)
Last I checked, you can represent 64 values with a measly six bits. (2^6 = 64).
But if you're searching for some pattern, representing each possible alternate codon as a separate bit has its applications.
Re:Bioengineering (Score:1)
That's fine, but the point is that one can make sort of a 'virtual gene' or 'genetic codon probability template', which happens to be optimized for a 64 bit computer, utilizing genetic algorithms. I agree with you that you can represent 64 values with six bits, which isn't exactly what I was refering to. The idea is to map each possible codon onto a bit of the packet which is going to analyzed by the processor. Probably, one will want to create a big-Indian or little-Indian (endian, whatever) ordering scheme.
For example:
AAA = 1000000000000000000000000000000000000000000000000
AAC = 0100000000000000000000000000000000000000000000000
AAG = 0010000000000000000000000000000000000000000000000
AAT = 0001000000000000000000000000000000000000000000000
etc.
and so forth. Therefore,
1111000000000000000000000000000000000000000000000
would equal ( Protein | AAA, AAC, AAG, AAT).
Great for optimizing a mainframe for crunching through a combinatorial space of codons, searching for proteins.
Re:Bioengineering (Score:2, Insightful)
So hence
-j
Re:Bioengineering (Score:1)
I agree that the problem can be implemented with a 23bit model. I believe that model is valid in many cases. However, I see the 64 bit model as being more accurate and representative of the underlying mathematics of genetics. Moreover, one can do the calculations with a 64bit model, and utilize a 23bit model as a check... if the 64bit model runs correctly, the results should be reducible to a 23bit explanation, and can be checked via another algorithm.
Also, I believe that the 64bit model can model a bunch of stuff that the 23bit model leaves out, including mutations, loops, reverses, and so forth. (i.e. aaa.aaa.CCC.ggg.ggg.ttt.ttt becomes aaa.aaC.CCg.ggg.ggt.ttt.ttX) I forget what that's called, but you get the idea. Deletion! Ah. Deletion, mutation, etc.
Anyhow, the 64bit model is really slick mathematically, and one can do really crazy cool masking and information analysis on the matrices which are formed.
Re:Bioengineering (Score:2, Insightful)
Re:Bioengineering (Score:1)
Re:Bioengineering (Score:2, Interesting)
Re:Genetic algorithms != bioinformatics (Score:2)
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.
Re:Uh... an algorithms textbook in a politics cour (Score:2)
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.
Calculus and Numerical Analysis (Score:3, Interesting)
Short answer: yes, if you're willing to get up to speed in the knowledge and vocabulary needed. And no, I think it's easier CS guy to learn biology than for a bio guy to learn how to program (yes, I speak from some experience - shudder).
I guess you can say that I'm in the bioinformatics field. My company does bio-simulation, which means to say, we build models of physiological processes in order to do experiments in silico. We also build the software to build the models. I'm in the core scientific computing group.
If you have a CS/EE background, you're probably all set in terms of programming, what you need is to bridge programming into the "bio" part of the world. This means numerical analysis and simulation, I know that when we were hiring, it was difficult finding people who could both program worth a damn and actually understood numerical methods/linear solvers/dynamic systems, which in general means being familiar with optimization + calculus and numerical approximation and numerical analysis.
So, I would pick up some texts/take classes on dynamic systems and numerical analysis and go from there. Bone up on your old calc texts also. If you can't give me the derivative of e^(4x+1) in less than 20 seconds, you've probably failed my interview for our group. You don't have to know a T-Cell from a macrophage, but you should know the relative merits of an explicit solver vs an implicit solver for solving ODE's.
If you're more interested in the genetics side, I don't think you'll need as much hard core numerical stuff, just more familiarity with the "genetic language", introns, t-RNA, codon, etc along with the problems and approaches in use. If you're interested in the protenomics (sp?) side of things, I would guess that you'd need more chemistry and physics to go along with the numerical stuff.
EnkiduEOT