Domain: uni-heidelberg.de
Stories and comments across the archive that link to uni-heidelberg.de.
Comments · 38
-
Re:How stupid
You forgot also to account for the screening effect of piling the coal ash as well.
This isn't relevant anyway, since most are not talking about living on top of a pile of coal ash. The issue is more general, uncontained release in the form of small percentage not removed by scrubbers or by leaching of daughter products from ash, neither of which is solved by piling (and can be made worse in the leaching case depending on the exact chemistry of the ash in consideration).
You may also be confusing permil with percent.
No, those previous figures were percentages, not from per mil. Estimates of the Suess effect from tree rings varies from 3-25%, because there are a lot of factors involved and it is not a straightforward measurement, and can be quite regional too. The C14 from nuclear testing is nearly gone now, but the global C14 levels are settling at a point a couple percent higher than they were before nuclear testing, and a lot of modeling has been struggling to explain this.
We really only care about the atmosphere since that is where the carbon in our food comes from.
The atmosphere is a very small fraction of the carbon cycle, and exchanges at least 20% of the carbon each year with other parts of the cycle. This is why you can see very short term region effects where percent change in CO2 equals percent change in C14, but longer term trends are much more complicated. This source covers some of the mess. The annual production of carbon dioxide by humans is quite small compared to the total carbon reservoir accessible to the carbon cycle, and while a lot piles up in the atmosphere, it does exchange. And this isn't even getting into that the low energy emissions from C14 have a much lower biological impact that other sources, despite being part of things like DNA, resulting in a much lower amount of exposure from C14 than from other sources.
-
Re:Still a long, LONG way to go...
Remember this [slashdot.org] story from ages ago? Remember how well that returned on its promises of creating a real brain? That was spike-timing dependent plasticity as well, and unsurprisingly it never did anything resembling thought.
The only place where the FACETS European project promised to create a real brain was on
/. The project goalwas to create a theoretical and experimental foundation for the realisation of novel computing paradigms which exploit the concepts experimentally observed in biological nervous systems
, according to its website [1].
As a matter of fact, this project has been a success, and led to the BrainScaleS European project, which
aims at understanding function and interaction of multiple spatial and temporal scales in brain information processing.
[2]. Again, there is no unrealistic/journalistic promises here.
[1] http://facets.kip.uni-heidelberg.de/public/goals/index.html [2] http://brainscales.kip.uni-heidelberg.de/
-
Re:Still a long, LONG way to go...
Remember this [slashdot.org] story from ages ago? Remember how well that returned on its promises of creating a real brain? That was spike-timing dependent plasticity as well, and unsurprisingly it never did anything resembling thought.
The only place where the FACETS European project promised to create a real brain was on
/. The project goalwas to create a theoretical and experimental foundation for the realisation of novel computing paradigms which exploit the concepts experimentally observed in biological nervous systems
, according to its website [1].
As a matter of fact, this project has been a success, and led to the BrainScaleS European project, which
aims at understanding function and interaction of multiple spatial and temporal scales in brain information processing.
[2]. Again, there is no unrealistic/journalistic promises here.
[1] http://facets.kip.uni-heidelberg.de/public/goals/index.html [2] http://brainscales.kip.uni-heidelberg.de/
-
Re:And yet-
The first poll is crap. The popularity of a university's web page have no bearing on the quality of its education and research performed. Until recently most German universities added their web pages as an afterthought and they were maintained by some IT admin sitting in a basement. I know that from first hand source having a friend working as IT admin at the University of Heidelberg. Having graduated there I always found its abysmally bad web presence a constant source of embarrassment.
There are some objective polls measuring research effectiveness using solid and well defined measures. And as one would expect the top tier well funded US research universities have a strong showing.
Yet, there is no strict correlation between good research and good education. Scanning the rankings listed in the related wikipedia entry does not show anything equivalent to the PISA effort for college level education.
The US does dismal in the PISA rankings despite of course the existence of some outstanding private and public high schools. In the same vein the fact that the US hosts a good dozen of the best research universities tells us little to nothing of how the gross of the US colleges are holding up in international comparison. The only thing we can be certain off is that it costs much more than in many other places to get an advanced degree (i.e. Canada, Europe).
-
Tech companies are helping tooThere is quite a few tech-companies helping too. Here is a small list:
- Inveneo. They are helping setting up a terrestrial wireless network. Because that is one of the things they do. http://www.inveneo.org/?q=haiti-response
- ushahidi is setting up and managing their crisis-reporting application here http://haiti.ushahidi.com/ more of what they do is here: http://blog.ushahidi.com/index.php/2010/01/15/haiti-update/
- The missing persons registry is here: http://www.haitianquake.com/ (google took that one over, it seems)
- There is a CrisisCamp for techies going on in DC today. They need GIS experts & programmers specifically. If you are in the area, here are the details: http://ow.ly/WQDD
- The university of heidelberg (yup, not a company) has put up a routing service based on Openstreetmap data: http://openls.geog.uni-heidelberg.de/osm-haiti/
- There is more on what the OSM community has done here: http://www.opengeodata.org/2010/01/14/haiti-openstreetmap-response/
In short, you don't even have to go to Haiti to be a helpful techie.
-
Re:You are subject to laws of where you live
Wrong. In Germany as well as in Austria 'Mein Kampf' is an illegal book prohibited under laws against glorifying and identifying with the National Socialist German Workers Party.
It may or may not be subject to the laws you've mentioned, but you're talking bollocks if you suggesting that that's the reason that only versions with a commentary are available. Oh look! Here's a copy of a 1939 edition of Mein Kampf being held legally in Germany.
The main reason you can't get it in other forms is simply that it's under copyright. In the library catalogue link above, notice the line saying "Keine Kopien möglich"? In Germany and Austria, as elsewhere in the EU, the copyright term on a book is life-plus-70 years. Therefore, it becomes public domain in 2015, and you will then be entitled to reproduce it and sell it in whatever form you damn well please. (Though at the time Hitler died I believe it was life-plus-80 years; I'm not sure if the change to life-plus-70 is retroactive or not.)
The copyright on the English translation has lapsed, which is why it's more readily available in English. A quick search shows that German bookshops don't carry the English translation either, but there's hardly much reason why they would.
-
Re:Modding system
I could maybe mod you up, or I could just reply, and at least you, as one of the few people who's paying attention, might get something out of it.
:)A few of the people in the authors list of that paper (maybe 4 or 5) are also in another research collaboration that's sort of a spinoff/descendant of the supernova cosmology project. I'm one of their collaborators in that other thing, and I asked one of them about 06F6.
His "best guess" was a neutron star (and your comment here is the only one to mention neutron stars seriously) - possibly formed by a "failed" supernova - which has accreted some material, maybe just gas it was passing through, and flared up/fused that material/blew that material off, or something.
Since SCP (like the collaboration that I'm in) is specifically interested in supernovae, it is likely this thing was found, and they weren't sure whether it might be a supernova, so they took a bunch of data on it, then ultimately decided it wasn't and wrote it up.
Unfortunately, it appears even the collaboration that discovered it aren't sure enough to say what it is, which isn't really surprising; there's a lot of specialization in astronomy and cosmology these days, and even though survey projects give everyone a whole bunch of cool data to analyze, someone who's looking for supernovae wouldn't necessarily also be able to tell you that a set of exposures of a chunk of space also showed an asteroid, a kuiper-belt object, or a whatever-this-is, let alone give you much insight into those other non-supernova objects.
The good news is that as the surveys really ramp up, with things like Pan-STARRS and the LSST coming, there will be a lot more data, and it will take less time to find the second, third, etc. examples of whatever weird new thing gets discovered. For example, the math for relating type Ia supernova (SN Ia) mass to light curve was worked out in 1993, it took ten years after that to find the first super-chandrasekhar-mass SN Ia, three years after that to find the second and one year after that to find the third (which is titled "a second example" because the second one found hadn't been formally written up and announced at the time, I think.
:)So whatever 06F6 is, it's likely we'll be seeing more of them... first of a class, yeah.
A neutron star farting out gas, which caught fire from a tiny spark created by a neighboring EM field, lasting one hundred days?
-
Re:Modding system
I could maybe mod you up, or I could just reply, and at least you, as one of the few people who's paying attention, might get something out of it.
:)A few of the people in the authors list of that paper (maybe 4 or 5) are also in another research collaboration that's sort of a spinoff/descendant of the supernova cosmology project. I'm one of their collaborators in that other thing, and I asked one of them about 06F6.
His "best guess" was a neutron star (and your comment here is the only one to mention neutron stars seriously) - possibly formed by a "failed" supernova - which has accreted some material, maybe just gas it was passing through, and flared up/fused that material/blew that material off, or something.
Since SCP (like the collaboration that I'm in) is specifically interested in supernovae, it is likely this thing was found, and they weren't sure whether it might be a supernova, so they took a bunch of data on it, then ultimately decided it wasn't and wrote it up.
Unfortunately, it appears even the collaboration that discovered it aren't sure enough to say what it is, which isn't really surprising; there's a lot of specialization in astronomy and cosmology these days, and even though survey projects give everyone a whole bunch of cool data to analyze, someone who's looking for supernovae wouldn't necessarily also be able to tell you that a set of exposures of a chunk of space also showed an asteroid, a kuiper-belt object, or a whatever-this-is, let alone give you much insight into those other non-supernova objects.
The good news is that as the surveys really ramp up, with things like Pan-STARRS and the LSST coming, there will be a lot more data, and it will take less time to find the second, third, etc. examples of whatever weird new thing gets discovered. For example, the math for relating type Ia supernova (SN Ia) mass to light curve was worked out in 1993, it took ten years after that to find the first super-chandrasekhar-mass SN Ia, three years after that to find the second and one year after that to find the third (which is titled "a second example" because the second one found hadn't been formally written up and announced at the time, I think.
:)So whatever 06F6 is, it's likely we'll be seeing more of them... first of a class, yeah.
-
Re:Unfortunately...
...TiO2 is basically poison.
Titanium dioxide is commonly in sunscreen and paints. A minority (including someone I know) have a allergic reaction to topical application.
As long as the paint doesn't secrete titanium dioxide into the air, the only problem I see is that allergic people have to where gloves when they paint.
-
Oops
I should have said "TiO2 nanoparticles are basically poison.
-
Unfortunately...
...TiO2 is basically poison.
-
"Other parts of the world"
My university is in the US, but how is this handled in other parts of the world?"
I studied physics in Heidelberg, Germany. During the first half of my first year (about 6 years ago), we had introductory courses in C (they liked to call it C++, but it really was glorified C). In the second half of the first year, there was a "technical informatics" (read: Hardware design) course, which involved every student designing a little 16bit chip which could decipher the DCF long-wave time signal. That part used mostly C, but had some bits were we had to gnaw through Assembler.
That was my formal introduction to computing. Later on in my course, I mostly used MatLab, and occasionally C. Sometimes I had to reverse-engineer old Fortran code. I wrote my Master's thesis in MatLab (even though it was a rather computationally expensive application. In scientific applications, the time saved during design time often easily makes up for the loss in computational efficiency).
Since I started my PhD, I've tried a lot of different languages, from MatLab to Java, C# Python and, recently, F#. Even though I was brought up with OSS (my laptop runs Debian next to Windows), I have come to value the rapid development capabilities of .NET (I know, it sounds crazy. Please try it out before you flame. Visual Studio is certainly the best (maybe the only good) piece of software Microsoft ever made). But I'm a theoretician, so my focus is on being able to rapidly change my code to incorporate new ideas. Experimentalists, who mostly just want to control their machinery, need to know more about Fortran, C, and on the high-level side, LabView and MatLab
I think my point is: It's probably a good idea to start with powerful low-level languages like C first, but don't overdo it. It's good if your students know about the existence of Assembler and Fortran, but the important point is that they lose their fear of computers. Nowadays, teenagers grow up with computers, but they never get to see behind the web 2.0 surface. Our generation grew up with text editors and batch files. They grow up with facebook. So it's important to give them a look behind the curtains. Let them feel the power of being able to control memory adresses. Once they have lost their fear of pointers, they can move on to use high-level languages that safe loads of design time, while being able to descend down into the architecture when it really counts. -
Re:Side Effects?
This subject is actually quite up my alley. Siemens Medical Solutions are offering a combined proton and carbon therapy facility. They use a synchrotron based accelerator that can accelerate protons and carbon (and also oxygen). The accelerator part is made by the Danish company Danfysik - where I'm employed as an accelerator physicist - based on a heavily modified version of the Heidelberger Ionenstrahl-Therapie (HIT) facility.
Most proton therapy machines are cyclotron based, making them cheaper than synchrotron based accelerators. However, they cannot produce beams of different energies (corresponding to different penetration depths), and one has to use energy degraders to obtain lower energies, which unfortunately also degrades the beam quality (increases its emittance).
Being a physicist and not a medical doctor this is not my area of expertise, but as I see it carbon is increasingly interesting and believed more effective than protons because the mean free path for carbon is around the distance between the two DNA spirals increasing the likelihood of a double-strand break - almost certainly killing the cancer cell. -
Re:Bah humbug
3.02 A thought contains the possibility of the situation of which it is the thought. What is thinkable is possible too.
Lugwig Wittgenstein
Tractatus Logico-Philosophicus
The question is how to let thoughts seem to be reality, though.
CC. -
Why 118? Well...
A lot of people seem to be dismissing this as without a practical use. However there is method to the seemed madness of making ever-bigger nuclei. Elements tend to be either stable or unstable - carbon is stable, uranium is not. This stability is caused by the arangement of protons/neutrons in the atoms' nucleii. I'm not exactly sure why this occurs - I'm a biologist, I'm not really meant to know - but whether or not a nulceus is stable or not follows a pattern determined by "shell-model" calculations (see here for the science bit).
So although making 3 atoms of 118 doesn't seem to amount to much, especially as it instantly falls apart, it's another step on the way to making th first of the synthetic heavy elements in a "stability island". It's thought that such a material could have strange and useful properties. Or it could be a complete waste of money and be boring as hell. I don't know, but that's the point of research at the end of the day...
-
Been there, done that.
The reason why all your ideas have not been realised is economical: It makes sense to develop a very expensive piece of technology that can help a lot of people, thereby bringing the price per treatment into an acceptable range. However, it doesn't make sense (yet) to use such complicated technologies to clean windshields because nobody is prepared to pay 200 k$ for a windshield cleaner (while a specialised ophthalmologist would certainly be prepared to pay as much for such a machine).
This technology is certainly no "pie in the sky". It's actually quite close to the market. I'd send you to this site, but it seems they spend more time on developing their machines than updating their site. :-) It's even more a pity that this press release is available in German only. Believe me, this is serious business. -
Re:What about other sorts?
Actually P~2*Q. Also, there are tweaks to Quicksort which guarantees O(nlogn) behaviour. If you need an efficient but somewhat general purpose quicksort I strongly recommend Jörg Schön's collection of C programs which include a simple include file that creates a very efficient sortinf routine, and coding takes seconds!!
-
Re:Worse than Vogon Poetry
Erm. Probably, if you promised not to make money off it, or promised to donate any money you made to charity.
There's a german effort underway to convert Lords & Ladies into a movie (this was previously covered on Slashdot). TP gave his blessing to that. All proceeds go to charity.
The project has already wrapped shooting and is in post production.
-
Re:Mini-series
This is a fan created movie, so don't expect this to be in the Legend class...
Wierd Systers -
Re:Approved?Actually it is:
From the making of:
During the film making process I got to know Catskind and David Hodges. They introduced me to the "Wadfest Bunch" and I learned there is a real and really working international Discworld Fandom. I also learned you can not just make a film out of every book you like even if it is just (and only) for fun and for your own private use. So I signed the contract with Terry Pratchett and...
...now the film is for everyone! -
Re:Take noteBetween the references to "the blob over Canada" (actually Ohio and environs) and to the one over "the east of Russia" (actually a country known as "China", including the city of Beijing), the geographic knowledge being shown here is a bit disappointing.
Some of the other "hot" spots visible in the larger version of the map correspond to Hong Kong (China), Seoul (Korea), Tokyo (Japan), Bangkok (Thailand), Delhi (India), Qatar (Qatar), Riyadh & Mecca (Saudia Arabia), Jerusalem (Israel), Moscow (Russia), Johannesburg/Pretoria (S.Africa), Venice/Milan/Genoa (Italy), Amsterdam/Brussels/Bonn (Netherland/Belgium/Germany), London (England), the DC-to-NYC region, Montreal & Toronto (Canada), Chicago, Minneapolis/St.Paul, Mexico City (guess), Denver, Santa Fe, Salt Lake, Phoenix, Vegas, and of course LA and San Francisco (all un-specified cities being in the U.S.A. of course).
-
Re:Take noteHere is the original map, or at least a bigger one.
I noticed a few interesting things on it. One being the Alberta oir industry, as you noticed. The other is the ripples over the Himalayas.
-
Re:Take note(thread hijack)
-
A few months ago, and other like technologiesI was looking to browse and copy files bnetween a variety of platforms in a really friendly way that wouldn't show up on most script kiddy scans. Gopher was the obvious protocol, unfortunately the server was a WinXP box and I was unable to find an appropriate gopher server for it. IE & Mozilla still support gopher://, does Safari?
BTW, for those reminiscing about text-based gopher don't forget GopherVR that came out just as http/html hit. An interesting experiment in 3D virtualization of online resources I've yet to see it equalled for other protocols.
Other now-obscure technologies from the same era:
-
Postscript Raytracer
-
Re:Screw resolution
Yes. At the University of Heidelberg, Germany, Physicists have developed a log-response CCD chip (covering 6 decades of intensity). They want to use it as the frontend sensor for their "tactile vision substitution system" (a machine enabling blind people to "see" with their fingers). The Log response is achieved by operating the sensor transistors in their non-linear range (very crude description, it's been a long time ago since I attended a talk about that project). Links to publications can be found following the above link.
-
Asteroid finding project?Crazy idea for a business: collect $1000 from people in return for a place in a queue [?] for getting asteroid names. Use the money to pay for the operation of an observatory. Send asteroid data to the Minor Planet Center. If the observatory is the first to spot an asteroid whose orbit is later determined, we choose a name for the asteroid based on the name of one the contributors in our queue.
Of course, this only works if you can find lots of people crazy enough to pay $1000 to get an asteroid named after them. But just think: you could get your name on the doomsday asteroid!
--
-
Re:Mirrors of the disputed content.
An other mirror...
-
Kernel 2.4 released to the public!According to a CNN story, Bill Clinton and Tony Blair annouced that the sources of the Linux kernel 2.4 will be released to the public!
Seriously, people. HUGEP isn't run by any goverment, and is a scientific project. Scientific means in that case: made by scientists working at public scientific institutions, like universities and such. Which automatically means that the human genome, once sequenced by HUGEP, will be published in Nature or Science or whatever scientific magazine they choose -- not the sequence per se, but due to publishing policy in these journals it will be accessible via WWW or on demand, as it is the case with all scientific research.Do you know that if you work at a university, and you find something suspicious (or want to repeat the research, or need it for your research, or are just curious) in a published article, you have a right to demand exact informations from the scientist who published it, including getting the original clones / organisms he used for the research? Of course, if the author works for a public institution. This is the major difference between them and such institutions like CELERA / TIGR.
Let me give you an example. This year an article appeared in Nature on a mutagenesis study of the small bacterium I'm working with. It was performed by associated scientists of one of those big commercial research centers. The article and information published on the web did not give you exact details as to where the reported mutations were placed on the genome, only -- which genes have been knocked out. A professor I know, who also works with these bacteria, wrote to the author to get the details of the study -- and never received any answer. This couldn't happen with an academic institution.
There is a book of a polish writer and Nobel prize winner, Sienkiewicz. It tells the story of the Swedish-Polish war from the XVII century. In one of the scenes, the king of Sweden offers to one of local polish princes that he will give this prince a certain polish teritory, which is occupied by the swedish army, if he agrees to colaborate. The prince answers -- "All right, and I will give you Netherlands".
What I want to say, they are giving away Netherlands: making an offer which is of no value just for the sake of telling it -- because it's not their science and because *of course* it will be released to the public. HELLO! This is not CELERA/ Perkin Elmer, for God's sake!
I will repeat myself, because I consider this matter very important: sequencing projects like HUGEP, payed by academic institutions do publish they data. Take a look at the Mycoplasma pneumoniae homepage -- the group I've been working in sequenced the genome and published it, and you can of course download all the data. Only on-going research projects, which have not yet been published in a scientific journal, are not public - yet.
Speaking of which: publishing the HUGEP data before the project is ready is giving a helpful hand to the privat counterpart of HUGEP - namely, Celera Research. And those are the "patent guys" in this case -- I would really like to see HUGEP ready before Celera is.
Regards,
January
-
Return to 1930's (1860's even)Who believe this Bull (market) suffer at the hands of latter day James Fisks
From london Financial Times Thursday Feb 24,article on Egg, a UK internet bank which is loosing money fast by enticing depositors with rates it cannot support (cant a city full of bond traders tell this is screwed?) says :
"In the short term no doubt, the Pru [Prudential, Egg's owners, a British insurer] will ensure Egg's stock flies. An engineered stock squeeze would certainly help, and predictably, Prudential is planning to list just 15 - 25% of the capital"
After the US saw its whole people belittled (and a world economy brought to its knees) by such machinations, simple manipulations such as those employed by Fisk were outlawed. Previous to Fisks demise, Vanderbuilt had been hailed as building a great empire upon such tricks. People will be in awe at such money - this is the nature of money. It has power over people who work for it. However it seems that we are no longer awake in vigilance against even the most puerile of deceptions.
-
Me too :-)Each time I see something about genes / DNA / cloning on
/. I have a bad feeling. Which usually gets worse after I've read the actual article.I think I know what the problem is: unless you are into a certain field, something like "scientists found now a way of switching genes on and off" sounds like a sensation, and "it seems that leptine plays an important role also in lizard metabolic regulation" does not - even though the first one is, roughly speaking, nothing but journalistic bullshit, and the second a real revelation.
In spite of my miserable English knowledge I keep submitting to slashdot articles from Nature science update and some other sites that are providing good scientific information. Unfortunatelly, they do not sound as interesting and enthusiastic as what you can read about biology in "XXN news for housewifes".
By the way, I work at ZMBH, Bujard, who developed the tet-system (which seems to work quite fine in many applications) also works here.
Regards,
January
-
Open source, patents and scientific communityThere is an article in today's Nature issue entitled "In praise of open software". It states, among other things, that "[bioinformatic] Tools [for genomics] that add value to genome data are to be welcomed, but as the licensing strategy being adopted by Celera Genomics becomes clear (see page 231), it gives new grounds for wariness." I know this is slightly off-topic, I just want to stress that the growing number of patents / license in my field of science is a matter of concern for many biologists, as it is clear from this article in the leading scientific journal.
Unfortunately, those of you who have no access to "Nature" cannot read the full article, but I put some exerts here. Actually, it was my today's slashdot submission (rejected, of course - I have never seen anything posted to slashdot referring to any good biological site). I thought the article is interesting, because it targets the whole scientific community (there is hardly a biologist out there not reading "Nature"), and is the first article in such a journal which mentions Linus Torvalds and Linux, therefore making these names known to a large number of scientists who never heard them before. In a certain way, it could bring Linux more publicity then an editorial in "Times".
Regards,
January
-
On men and MycoplasmaHello, I'm January and I work on Mycoplasma pneumoniae genomics and transcriptomics. I want to add a few words on C.J. Venters revelations.
Mycoplasma genitalium, sequenced by Fraser and Venter, is in principle a deletion mutant of Mycoplasma pneumoniae, sequenced by people from the group I'm in. That means, it lacks a few genes M. pneumoniae still considers interesting for general survival, but all in all those two species are highly similar, with the same genetic apparatus etc.
Both species can be subjected to random transposon mutagenesis - you shot at the genome with a tiny little thingie called "transposone", which randomly destroyes some gene. If the gene destroyed is important, such a cell will not grow and reproduce. Therefore in the mix you have only mycoplasmas, whos important genes are preserved, will grow. You can then use the Polymerase Chain Reaction to amplify and examine what genes specifically got destroyed - that means, which genes are not necessary to grow
...under laboratory conditions, of course. And ceteris paribus, that means - all other conditions being equall. Especially, other genes being intact.Venter tries to a) make the impression that he did the work b) he's got a strain with xxx genes "switched off", which is not true. We only know that all of this 150+ genes are not needed for mycoplasmas to grow if other genes are intact. The way to constructing the "minimal cell" is long, if you want, I can get into details.
By the way, this information has three to four years, and Venter started talking about his "custom-made" M. genitalium about two years ago.
The whole project will make huge publicity and a very little contribution to science. First, "essence of life", my foot. A piece of RNA with a couple of molecules surrounding it is perfectly capable of proliferating, evolving and making you deathly sick, providing it finds enough cells to proliferate within. Intact mycoplasmas need a lot of organic substances in their growth medium - you have to add bovine serum. Essentially, the border between something quite inanimated like virus and a living cell is smooth. Next, this "crucial genes" will be different for different systems and assemblies. Finally, you have assembly this living cell out of "living" molecules - it needs polymerases, ATP, lipids, synthetised DNAs and RNAs and so on just to start living. Ian Wilmut put dead DNA into a "dead" (unable to proliferate, without genetic material) cell, so did he created new, artificial life? Bulls..cience. Artificial life will be when you start with natural, inorganic and simple molecules. Assembling existing parts has not much in common of finding an existing formula of life, especially because it will not help you understand how those parts work! And this is a different research (proteomics/transcriptomics) and it is really a way to go before there will be an appriopriate article on
/.. By the way, /. publishes lately a lot of cheap sensations. Sorry to say it.Regards,
January
(from the JanKatz-Falls-For-Every-Commercial-Trick-Dpt.)
-
TIGR, HUGEP and genomicsHello, my name is January and the group in which I am doing my Ph.D. thesis sequenced in 1996 a bacterial genome (Mycoplasma pneumoniae). Since we are into genomics, transcriptomics and all other -mics I know at least a little about the way it works - although on a much smaller scale.
First issue: could distributed computing help? My answer is a brief "no". First, the bottleneck is on the experimental side - getting the sequences, and not putting them all together. Second, although you need quite a lot of computing power to do so, much of the job must be revised and checked by humans, i.e. there is a lot of skilled manual work to do - you have to have "an eye" for the sequences. But the first point is more important.
Now, TIGR, the commercial alternative to the Humane Genome Project has sequenced more organisms then any other scientific group in the world. Craigg J. Venter seems to be very efficient and hard working guy. Even if you don't like the idea of making money with patents in this area the scientific community owes him a lot - he was the one to sequence the first organism, to sequence Helicobacter pylori and many, many others. On the other side... you know, when M. pneumoniae sequence was about to be published, it was supposed to be the first Mycoplasma sequence. But Venter was faster with Mycoplasma genitalium - and he kept it quiet, so noone involved in sequencing those organisms actually knew there is a race. Now Venter claimed to be able to complete the human genome with much less effort and much less $$, and considerably faster then the HuGeP. I'm not sure whether he is able to do so or not, because it depends chiefly on the "hardware" side - the new Perkin Elmer automatized sequencers they are supposed to use.
Anyway, the question is, whether it is good or bad if Venter sequences the human genome. In my opinion - it's OK. The Hugep is somewhot different in its purely scientific interest, and I'm convinced that they will produce data of much higher quality. On the other hand, human genome has a considerable variation, so two genomes are better then one. I would not be very concerned about the patent issue, because it will come anyway (because of **!'*%$! american and international patent law) - even if TIGR would not sequence the genome, someone takes the output of the HUGEP project and will patent the same sequences Venter would. Venter just wants to gain a little time for evaluating the sequence before releasing it to the public.
And of course, not the _sequences_ are patented - what is patented, is the usage of modification of a certain sequence for medical purposes, or a certain enzyme as an aim in medical treatment.
Regards,
January
-
PDF alternative and copyrightsFirst - I don't think this is a copyright violation - the book has 235 pages, and only 10% of them are reproduced, which is roughly what you may reproduce from a book or article without permission (as far as I know, of course).
Second, BEWARE. This page is lame - all gifs on a single page, and they are HUGE. For my own purposes I downloaded them with wget, converted to ps and finally produced one single PDF file. You can download it here. This is my student account, and in Germany, so if someone can put it for all the slashdotters in USA on an american server and notify me I would be grateful.
Regards,
January
-
Re:Thanks -- informed analysis usefulOK, I was thinking about creating such a webpage for a long time. Unfortunatelly, my english is... pathetic. Nevertheless, I did a primer, an alpha version, a grin-duck-and-run page:
The Biogeek page. Well, if anybody is interested, I might get on with the idea... although... I really don't know... What do you think?
Regards,
January
-
More on biochipsIt happens that my working group at the Center for Molecular Biology, Heidelberg is exactly into this thing - microarrays, biochips & co. So I might tell you some words on how does it work and why I think this is not the best solution for MT diagnostics in Russia. First, the preliminaries (if you slept at your biology class, try looking at Everything
:-). If you have a single stranded DNA sequence, then you can use it to fish out the so called complementary DNA sequence from a mixture of different molecules - the both single strands hybridize and make a double strang. It is easy to synthetise virtually any DNA sequence you need. Now, imagine that you want to detect whether in your mix there is a certain DNA species. What you do in the biochip technology is to bind your synthetized DNA on a glass plate (biochip) or nylon membrane (microarray) and label your unknown mixture of DNAs - say, a fluorescent molecule is attached to every DNA molecule in the mixture. Now, you wash the glass chip with the mixture: only the complementary DNA is specifically bound to the probe immobilized on the chip (or array). Now you wash with another solution - and what remains and can be detected by a fluorescence-detector will be the probe you are looking for.The clue about this system is that you can bind to your glassware an immense number of different probes, and so probe for different genes or regions of the genome (in fact, we are using this system to detect mRNAs - to see how an organisms expresses its genes).
But this system has one major disadvantage: it is not nearly as sensitive as other methods - the PCR / RT-PCR, for example. That means, to identify the MT strain you have first to raise it on a culture medium, because direct patient isolates will not provide enough genetic material to acomplish the task. And rasing MT is not easy.
It seems to me, someone wants desperatly to make the news: biochips have made the news a couple of years ago; right now commercial systems for many different tasks are available since many years. Check an issue of "Nature" for advertisments
:) you can have the whole yeast genome on a small piece of glass for a couple of $$.What's more, the system described is very, very expensive, and I doubt that it is therefore suitable for diagnostics in Russia. PCR-based systems are much cheaper - though not allowing to check a couple of thousands genes with a single reaction - but much better suitable for cheap and quick MT diagnosis.
It is, of course, quite possible that the EETimes got everything wrong and it does make sense after all. Journalists
;-)Regards,
January
-
take a look!
Gimp
X-Accountant (Quicken Clone)
Quicken for linux?
Flight Gear
One educational program:
Nightfall
look before you speak, this took my 3 minutes to find. :)