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• T Rex International Paleontonomics Experiment (TRIPE)
• Credit Given to Ross Geller
• Genes "identified" included TINY_ARMS and SMALL_BRAIN
• DNA was said to be extracted from a fossilized big toe

Of course, this was all placed on April 1 of approximately 2002, and promptly removed on April 2. It was understood to be a hoax, but still a very funny one.

Just a minor correction, but since I work there, for your #3 it's 'TIGR', not 'IGR'. Both the ranking and its description in the article is a little funny, though. :)

http://www.tigr.org/

Its not as if the NCBI is the only ones publishing genomes. taking a few examples from our useful links page

• UCSC
• Ensembl
• TIGR
• GenomeNet
• GeneLynx

Its Google is not even doing something new type in a human gene (say ABCA1and you will get taken to the gene data pages anyway

The only reason why they picked on Google is that it would get headlines, now move along nothing to see here

I wish that the Slashdot submitter had linked to the original article instead. It doesn't have these crazy advertizing gimmicks embedded in the text.
http://www.tigr.org/news/pr_12_02_05.shtml

No, I'm NOT talking about the ads at the bottom under the 'Ads by Google' disclaimer. I'm talking about the hijacking of the hyperlinks themselves as an advertising gimmick, a gimmick which is introduced at the cost of the article actually having any hyperlinked text.

You're telling me that I should read all the disclaimers at the bottom of every page first? That's a joke, right? Or are you one of those people who thinks that the answer to dealing with confusion on a page is to educate the whole world as to how to not let a confusing page confuse them instead of simply fixing what's confusing on the page? I know people who feel the way you do. I fired one of them last week.

I'm running Firefox. Let me know how to disable what this web site's screwing around with the hyperlink concept. I'm sure a lot of us would like to know. On the other hand, I'm betting that you don't know how to do this, and that it can't be done, and that you are just bullshitting us all (or thinking that you are, anyway).

1. This is an example of argument from incredulity, because irreducible complexity can evolve naturally. Many of the proteins in the bacterial flagellum or eukaryotic cilium are similar to each other or to proteins for other functions. Their origins can easily be explained by a series of gene duplication events followed by modification and/or cooption, proceeding gradually through intermediate systems different from and simpler than the final flagellum.

One plausible path for the evolution of flagella goes through the following basic stages (keep in mind that this is a summary, and that each major cooption event would be followed by long periods of gradual optimization of function)...

(see site for seven step path)

2. The bacterial flagellum is not even irreducible...

3.Eubacterial flagella, archebacterial flagella, and cilia use entirely different designs for the same function. That is to be expected if they evolved separately, but it makes no sense if they were the work of the same designer.

• Why humans and chimps don't just share nearly all of our genes, but nearly all of our broken genes (and why human gene 2 looks like exactly like chimp genes 2p and 2q fused together, nonfunctioning broken bits of telomeres right at the fuse point).
• Transitional forms like reptiles to mammals, dinosaurs to birds, and, yes, apes to human.
• Atavisms, Biogeography, Convergence of independent phylogenies and the other 26+ evidences detailed in 29 Evidences for Macroevolution"-- each one individually usable for predictions about (or for falsifying) evolution.

That bacteria would be Deinococcus radiodurans. Literally, 'strange berry that withstands radiation'. Its trick is actually several copies of important genes on different chromosomes, so that it can line up a good copy with a bad one and rapidly make the repair to damaged DNA. From this site:

Among the many characteristics of D. radiodurans, a few of the most noteworthy include an extreme resistance to genotoxic chemicals, oxidative damage, high levels of ionizing and ultraviolet radiation, and dehydration. The ability to survive such extreme environments is attributed to D. radiodurans ability to repair damaged chromosomes. It is known that heat, dehydration and radiation causes double-strand breaks in chromosomal DNA. D. radiodurans will repair these chromosome fragments, usually within 12-24 hours, using a two-system process with the latter being the most crucial method. Initially, D. radiodurans use a process called single-strand annealing to reconnect some chromosome fragments. Next, D. radiodurans use a process known as homologous recombination, where a modified yet efficient RecA protein patches double-strand breaks. RecA protein works by cutting usable DNA from another molecule and inserting it into the damaged strand.

However, these repair methods alone are not unique to D. radiodurans, which therefore cannot account for its radiation resistance. The aforementioned statement has led scientists to propose the "Life Saver" hypothesis. The hypothesis states, that in order to speed homologous recombination, D. radiodurans align copies of its genome so that identical DNA sequences are near each other. This proposal is now entirely possible due to the verification that D. radiodurans genes come packaged in four distinct circular chromosomes, thus giving stacked loops of DNA and resembling a Life Saver. To add to the list of radiation protective traits, D. radiodurans also possess carotenoid pigments, oxygen toxicity defense enzymes, and a distinctive outer membrane. First, carotenoids, which cause red pigmentation, are thought to act as free radical scavengers, thus increasing resistance to DNA damage by hydroxyl radicals. Next, high levels of enzymes such as superoxide dismutase and catalase both play a role in effective defense mechanisms against oxygen toxicity. Finally, a cell wall forming three or more layers with complex outer membrane lipids and a thick peptidoglycan layer containing the amino acid omithine also serves to protect D. radiodurans from lethal doses of radiation.

Google search:
http://www.google.com/search?q=M.+genitalium&sourc eid=mozilla-search&start=0&start=0

Best link in search:
http://www.tigr.org/tdb/CMR/gmg/htmls/Background.h tml

The jist of it is, it's a simple prokaryotic creature that has been fully sequenced. The full genetic sequence is about 0.54MB of data.

Government agencies and researchers are constantly doing things which can put companies out of business. Let's see current stories on CNN...

• Genetic research may help anthrax mystery. That's bad for the drug industry, hospitals and cleaning services.NSF funding, using results of research from 3 US and a UK government agency.
• Judge orders VeriSign to stop ad campaign. That sounds a little restrictive on business.
• Wearable computers enhance the world. Threatening tour guides, makers of sprinkler system maps, pipeline markers, and jet engine mechanics.
• ISPs seek to void ruling on police searches. ISPs are complaining that a dozen police hanging around each day could be bad for business.
• House set to renew welfare program. Bad for lawyers, companies that need cheap unskilled labor, companies that pay taxes used for welfare, competitors of companies which print welfare forms, the extinct creditor's prison industry.
• GOP leader skips Bush meeting over Crusader. Millions of dollars cut off from companies working on Crusader, and competitors who weren't getting those millions.
• White House won't defer import duties. Anyone need explanation of how imports or duties affect businesses?

This is a wonderful announcement, but as I can see from the lack of comments in this discussion, not an exciting one.

About 5 years ago, the unveiling of a newly sequenced bacterial genome was cause for great celebration. Today, there are over 40 species of bacteria whose genome has been completely sequenced. While the addition of one more "bug" might not be that exciting nowadays, one must realize that the compilation of this kind of information has far-reaching effects in the fields of medicine and biology.

For more info, check out The Institute for Genomic Research

Therefore 18000+ genomes could be fitted into 1TB. I guess compression would allow this to be increased somewhat.

"...In the paper, published in the December 10 issue of Science, the minimum number of protein-coding genes required for cellular life in the laboratory is between 265 and 350. Surprisingly, this minimal gene set includes about 100 genes of unknown function. This finding draws into question a prevailing assumption that the basic molecular mechanisms underlying cellular life are understood, at least in broad outline..."

Is it feasible to determine which genes are common to all life forms currently living on the planet The answer may lead some insight into the question of what is the minimum requirement for life.

IAAG. This question is more philisophical than scientific. Define life first. You can generate self-replicating molecules using themselves as templates using RNA only, under specific in vitro conditions. Is that life? Generally speaking, organisms (i.e., one or more cell, not viruses) adapt to an environmental niche that they occupy and retain what genes they need to survive in that niche. Since each niche is a different microenvironment, all organisms have different genes (evolutionary adaptation).

However, to answer your question somewhat more directly I recall that mycoplasma has the currently known smallest genome of any organism, with 580074 base pairs of DNA, and 483 genes. See The Mycoplasma genetalium Genome Database for more info.


---
Santa Claus: "Ho ho ho!"

Having fun with genomics::
The entire genome of Deinococcus radiodurans is freely available at TIGR.
Enjoy!

TIGR != CELERA! TIGR is a non-profit research institute funded by grants TIGR CELERA is a for profit company funded by stock market and Perkin Elmer. CELERA
TIGR data is publicly and freely available, just go look at their website/ftp... tons of good stuff there.
Yes the head of TIGR went on to found celera but that hasn't changed TIGR. Except maybe that the scientists who remained at tigr when they likely were offered jobs at celera must be quite dedicated to doing non-profit public research

Anonymous Coward

Those are very useful references, as is the PubMed link somewhere below this and the links to the Sanger Center (EBI) etc. However, the poster of the question appears to be concerned also with corporate research in this area, and surely there is no more important site in this regard than TIGR:The Institute for Genomic Research. This is the website of the largest, fastest sequencing factory in the world. It has good resources detailing the completed genomes of many organisms. TIGR is a private company that has beaten many of the "open" genome projects. They've been notably succesful at churning out sequences before largely government backed projects due to their capital investment that is banking on being able to make money from patenting sequence. They've pushed the envelope and stirred everyone up which is great, but they're also an example of a privately funded "land grab" that may impoverish the rest of us.
--Crush (posting as AC because I moderated)

If B. subtilis and D. radiodurans are Martian, then just about everything else on earth is Martian in origin as well. Yes, the two organisms have some incredible survival abilities--but biochemically they just aren't that different from terrestrial life.

You can get sequence info on the genome for D. radiodurans here, and B. subtilis here.

Basically, science knows a lot about these two organisms, and what we know suggests that they fit right into the phylogenetic tree. And even if they didn't, the fact that we can get a genome sequence *at all* would tell us they are probably related to terrestrial life.

Sorry this is 16 hours after first post and too late to get moderated up... but for those hackers who want "code," or any download scavengers wanting the raw gene sequence data for M. Genitalium, I found it at ftp://ftp.tigr.org/pub/data/m_genitalium/

Will this finish a task? No, it is just a beginning - having the sequence, the real work starts: searching ORFs (Open Reading Frames - sequences which could possibly be genes), running database searches, and slowly passing to the most exciting fields of modern molecular biology - from genomics to transcriptomics and proteomics. Transcriptomics is looking for genes, which actually got expressed, and proteomics - similarly, looking for expressed proteins. Making transcription / translation (translation is the process in which proteins get synthetized) profiles can lead us to 1) function of proteins (e.g. protein X. is expressed under this and this conditions, so it must take part in this and this metabolic response) 2) regulation - DNA is a single strand, but various enzymes are present in various copy numbers under various conditions.

Those are enormous projects. A lot of work has to be done before the raw sequence will actually be of any use; nethertheless, it is a milestone of molecular biology and will be a fine achievement for the end of our century.

Another project will be to determine the variability of human genome: screening for different gene allels, mutations etc. This will be one of the most important goals in human genomics in the next few years.

Whats on the catch... erm, chromosome 22? 22 is 33,400,000 bases long (Mycoplasma pneumoniae, one of the smallest bacteriums, has about 816,394 bases). It contains several already known genes responsible for various genetic disorders, and possibly a gene responsible for certain types of schizophrenia.

By the way, a much better source of information is the Nature science update page - the original scientific publication has been published today in Nature.

Regards,

January

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

The idea of making a portal out of it is interesting but BLAST has been around for some time...

True. There's A LOT of sites dealing with various facets of genetic information. Starting from databases containing 'raw' DNA sequences coming off various genome sequencing projects (no, it's not only human; genomes of twenty or so organisms have been or are being sequenced at the moment) all the way to servers trying to interpret the data. Just check Pedro's list or one of the mirrors in Germany or Switzerland. And note that this is not so current (in fact nearly 3 years old) but already pretty long list...

The first thing consideres gene therapy, cloning and such. Although I personally believe that human cloning - say, human cloning from somatic cells, as opposed to cloning the embryo - will remain fiction for a long time, not due to ethical or technical reasons, but because it's not useful - I also think that the further evolution of medicine and biology will go in the direction depicted by Mr. Sterling in "Holy Fire". In a few years the human genome will be sequenced - either by the Humane Genome Project or Craigg Venter from The Institute for Genomic Research, and this will provide the basis for an extensive research on the functioning of a human cell. Sooner or later the gene therapy becomes something widespread, and I'm not even talking about super-human beings or creating superintelligent kids, but just mending all the small defects a person inherited from his parents. You would be amazed if you knew how many of such little defects you have :) I wonder what do
you think, realistically, about future of medicine - will it be something like what was described in "Holy Fire"?

Another thing I wanted to ask Mr. Sterling (my esprit d'escalier be damned) is, what does he think about the Internet as an experimental field for memetics. A meme is a term coined by Richard Dawkins (the samed who first used the expression "selfish gene") back in the 80s, and it described what is also know as a "virus of the mind" - a small portion of information, which spreads from one human to another, replicating and evolving, using the human brain as a host, but not providing any advantage to the person who spreads it (rather a disadvatage). The first time I started getting the "Good Times" message to my mailbox, I told myself - well, here you have a perfect virus of the mind, spreading and evolving, and relatively easy to trace. Right now there are plenty of ideas on the Internet, which spread like a virus, and it could be possible to design some memetical experiments.

What do you think about memetics? Do you think it is worth using it to examine the cultural evolution?

Regards,

January

Well, you do not assemble simple subroutines, but carefully select very complicated subtroutines, known already to work in other programs for ages.

And yes, you will get many bugs, but almost all bugs would cause the program to crash, and you'd just forget about it. The changes you create a program that would find its way onto the net and do something dangerous are really slim (not to be neglected, though).

You are of course only allowed to do this if the license of the chosen subroutines permits this. Well, Craig Venter has patents on many genes, so he should have no problems...

But i would say we really should start a serious open source movement here, i mean, patents on genes? Look at the license for human genes from TIGR, for crying out loud. This whole science thing started as open source, and it should have stayed that way. What if Newton patented the gravitational constant?