Saturday, October 09, 2004
Thursday, October 07, 2004
Fruitflies really do like bananas
The Nobel prize for medicine went this year to Richard Axel and Linda B. Buck who described the genes and cells of the olfactory system.
Interestingly, the expression of functional olfactory receptors, an important subclass of G-protein coupled receptors in tissue culture has proven difficult.
As a result, the premier genetic model organism, Drosophila melanogaster, is now gaining acceptance in olfactory research.
Recent (well, last year) research finally allows us to say with certainty that while time flies like an arrow, fruit flies like bananas.
SN-GC is the method employed: single neuron electrophysiogical recordings from living flies as detectors for gas chromatography columns.
This allowed the establishment of a preference for (more neuronal firing) odors from rotting fruit, and yes in particular from bananas.
Human olfactory receptors have been expressed in C. elegans, so it seems likely that the functional expression of human olfactory receptors could be achieved in antennal drosophila neurons.
If this can be shown, it would plausible that with some effort the full array of human olfactory receptors would be expressed in drosophila.
If not in D. melanogaster, another method will eventually be found for functional expression of hORs, and then the full complement of ligands for each receptor can be defined.
If flies are used, an updated descendant of the SN-GC technique could be used.
The matrix of hOR response to a particular mixture of odorants (e.g. a perfume) could then be used to define odors in support of patents and trademarks.
Confirmation that time's fun when you're having flies awaits further work.
Articles I couldn't shoehorn in above.
Tuesday, October 05, 2004
podcasting
Okay, I've had a chance to listen to a bit of those 720 Mb of downloaded mp3s that came in by default with installation of pyPodder. It is painful to listen to, and I couldn't find anything in there worth keeping.
Take my word, you won't be missing anything by skipping it all. I'm still interested in the concept as a way to update the compute farm, but as far as personal use is concerned, I'm not going to bother.
Take my word, you won't be missing anything by skipping it all. I'm still interested in the concept as a way to update the compute farm, but as far as personal use is concerned, I'm not going to bother.
File distribution methods
A problem faced by all large scale compute farms is distribution and maintenance of large amounts of data. For bioinformatic compute farms, this is the sequence data that underlies all other analyses.
Do methods of distributing mp3 encoded audio such as RSS 2.0 enclosures, BitTorrent and scripted clients used in podcasting offer an alternative method for distribution?
I'm currently trying pyPodder. Works, but on my first spin it downloaded 720 Mb of spoken word mp3s. Now why is it we all need broadband again?
Other refs: RSS|ipodding
Do methods of distributing mp3 encoded audio such as RSS 2.0 enclosures, BitTorrent and scripted clients used in podcasting offer an alternative method for distribution?
I'm currently trying pyPodder. Works, but on my first spin it downloaded 720 Mb of spoken word mp3s. Now why is it we all need broadband again?
Other refs: RSS|ipodding
network analysis using tools from bioinformatics
Slashdot follows up on a previous article describing use of sequence analysis methods taken from bioinformatics to enable network protocol analysis.
The actual source code is now available at Protocol Informatics. They seem to be taking C++/python approach, and have a rather fresh look at bioinformatics, with a few interesting links.
I've signed up for the mailing list and downloaded the code.
The actual source code is now available at Protocol Informatics. They seem to be taking C++/python approach, and have a rather fresh look at bioinformatics, with a few interesting links.
I've signed up for the mailing list and downloaded the code.
Why Information Biology?
Why not bioinformatics, or computational biology, or systems biology? Information Biology is the phrase that best fits my own particular slant on computation and living systems. I was captured at an early age by the realization that DNA and proteins can be beautifully summarized as strings of alphabetic characters. This now common place representation still amazes me.
Bateson defined information best: news of difference that makes a difference. For information to exist, there must always be an entity to sense and care about differences. The world of the living is a place "... where distinctions are drawn and differences can be a cause", which is to say where information is used.
Shannon, in describing how to measure information, was careful to note that "semantic aspects of communication are irrelevant to the engineering problem", ie he avoided completely the question of meaning. In his definition the quantity of information obtainable on receipt of a single message is proportional to the number of equipropable messages that could have been sent. If only two such messages are possible, receipt of one offers the smallest possible piece of information. Note the clear differentiation of possible quantity of information from actual information. Shannon talks about how much information could be sent, not whether the message was meaningful. From the engineering perspective it doesn't matter. Unfortunately, after this careful beginning, first Shannon and then most others have used the word information to refer to this quantitative capacity for transmitting or holding meaningful information. Too bad!
Many if not most references to information are hopelessly confused due to the failure to distinguish Bateson's meaningful information from Shannon's capacity for information, resulting eventually in the sad occurrence of such oxymorons as "useless information" or "information overload" . While it's alright to call a pint of beer a pint, since no one will confuse a unit of liquid measure for a refreshing beverage, it's quite a different story with differences that make a difference as opposed to the ability to write them down in one place. No one can see the difference between a zeroed hard drive and one filled with an entire collection of music or all the secrets to the construction of advanced weapons, but the difference is real. The size of the drive determines the amount of music or number of secrets that can be stored, but of doesn't indicate whether they are there - this should be as obvious as the pint and the beer, and yet it is often and profoundly ignored in common discussion. There should really be two words, one for Bateson's information (the music and the secrets), and one for Shannon's (the size of the hard drive), but at present we have only one. Readers beware!
Bateson defined information best: news of difference that makes a difference. For information to exist, there must always be an entity to sense and care about differences. The world of the living is a place "... where distinctions are drawn and differences can be a cause", which is to say where information is used.
Shannon, in describing how to measure information, was careful to note that "semantic aspects of communication are irrelevant to the engineering problem", ie he avoided completely the question of meaning. In his definition the quantity of information obtainable on receipt of a single message is proportional to the number of equipropable messages that could have been sent. If only two such messages are possible, receipt of one offers the smallest possible piece of information. Note the clear differentiation of possible quantity of information from actual information. Shannon talks about how much information could be sent, not whether the message was meaningful. From the engineering perspective it doesn't matter. Unfortunately, after this careful beginning, first Shannon and then most others have used the word information to refer to this quantitative capacity for transmitting or holding meaningful information. Too bad!
Many if not most references to information are hopelessly confused due to the failure to distinguish Bateson's meaningful information from Shannon's capacity for information, resulting eventually in the sad occurrence of such oxymorons as "useless information" or "information overload" . While it's alright to call a pint of beer a pint, since no one will confuse a unit of liquid measure for a refreshing beverage, it's quite a different story with differences that make a difference as opposed to the ability to write them down in one place. No one can see the difference between a zeroed hard drive and one filled with an entire collection of music or all the secrets to the construction of advanced weapons, but the difference is real. The size of the drive determines the amount of music or number of secrets that can be stored, but of doesn't indicate whether they are there - this should be as obvious as the pint and the beer, and yet it is often and profoundly ignored in common discussion. There should really be two words, one for Bateson's information (the music and the secrets), and one for Shannon's (the size of the hard drive), but at present we have only one. Readers beware!
Subscribe to:
Posts (Atom)