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Fugu May Be Key To Human Genome
sulli writes ; "If it doesn't kill you first, it may get you a Nobel Prize. The fugu (puffer fish), best known for being a delicacy in Japan despite being poisonous if improperly prepared, has a very short genome (400M base pairs) compared to that of humans (3.5B base pairs). Says a sushi fan at DOE: "[W]henever researchers have gone into the fugu and looked for human genes, by and large they've found them." Info from a related project in the UK is here."
it would explain Dizzy Gillespie! ;)
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Shit, it was your sig. Damn! Still a funny idea.
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Says a sushi fan at DOE: "[W]henever researchers have gone into the fugu and looked for human genes, by and large they've found them."
The only explanation is that someting funny has been going on between the Jackes Coustau team and female fugus. I don't blame them, 6 months expeditions out to see can take a toll on you.
~~~Please pass the salt, I hate unsalted MD5s
I don't think this is too far off the mark. Evolution is not an optimized process, and a lot of the unused and useless "code" would be "commented out". There is no need to clean out these unused pieces, because it's not getting in the way, and some of it will invariably come in handy sometime in the future.
It's taken millions of years for complex life to evolve -- that's a lot of commented out code.
DNA polymerase, the enzyme which replicates DNA, isn't capable of getting all the way to the end of the chromosome. As a result, when you duplicate the DNA during cell division the copy you end up with is shorter than the original. This has obvious problems if you replicate enough. The solution is to code for an enzyme called telomerase which is capable of adding extra DNA to the end of a chromosome to get it back to the original length. This DNA doesn't code for anything (in most organisms it's made up of highly repetative sequences), and is only there to make sure you don't end up with shorter chromosomes than you started with.
Interestingly, Drosophila Melanogaster doesn't do this - rather than have an enzyme that adds DNA, transposable elements (short sections of DNA that are capable of moving themselves from place to place in the genome. Very cool.) jump in from further down the chromosome and replace the removed bits directly. AFAIK, it's the only organism known to do this - even yeast has a setup similar to the one we use.
The Minimal Genome Project tried to answer this question by disrupting genes in M. genitalium until they had an organism with a minimum number of genes that was still viable.
My girlfriend and I were visiting NYC this weekend to do our Christmas shopping. We had reservations for Japanese food on Saturday. The main course? Fugu sashimi!
The fish is sliced very thin, with each bite-size piece arranged around a large plate as the petals of a flower. The sushi chef places some shredded fugu and fugu skin at the 5-7 o'clock quadrant of the plate. A small mound of finely chopped scalions and pickled radish make the centre of the flower.
To eat it: Mix the scalions and radish with thinly diluted soy sauce. Squirt some Japanese lime over the fugu. Wait a minute or so, then pick a piece up with your chopsticks, dunk it in the sauce, and eat it slowly. The result? Delicious. Very delicate flavour, and the lips, palate and tongue tingle and get a bit red.
My girlfriend and I both enjoyed the fugu very much. She freaked out a bit when I told her about the tetradotoxin; she was about halfway done with her sashimi plate. Nevertheless she raved on it and would definitely order it again.
I live in San Francisco, and there are one or two places here who supposedly serve fugu; they never seem to have it, though. If you happen to be in NYC and want to try this, check out Chikubu Restaurant. It's on 46th or 45th (?) between 5th and 6th Avenues. You will need reservations; also, we recommend the sashimi. There is something else they make with it (I don't recall what) but I figure sashimi is the best way to go. The price? $70/plate. I believe fugu is available (in Japan or elsewhere) from autumm to spring only.
Cheers!
Ehttp://eugeneciurana.com | http://ciurana.eu
Just because the gene is there does not mean it is active. Remember that every cell in your body contains the exact same genetic information. It's just that different parts of the genes are active in different cells.
The cells in your heart, hand, brain, muscle and liver are completely different in their functionality, despite being created from the same DNA.
What you (and for some reason the author of the article) fail to realize is that there is not a continuous mapping between the size of genetic data and biological complexity. Quite often evolution occurs not by increased complexity, but by shedding un-needed functionality. Some primates have tails as well as more functional feet than humans do. Certainly that requires more data. So in that case, part of the evolution towards becoming human involved the discarding or deactivation of those active genes.
We may still have that data somewhere in our DNA, it's just not switched on.
-... ---
Simply remove the wet/worn out footwear and apply dry/new footware.
134340: I am not a number. I am a free planet!
("Fugu me!!!", "My expert hands are busy!!" and other great quotes).
And now back to my pointless existance.
("Give me an open face club, sand wedge" :)
"Hmmmmm, open face club sandwich"
"I'll take the red pill. No! Blue! AAAaaaahhhhhhhhh"
- Monty Python meets the Matrix
The puffer fish does seem awfully human. Most genes code for biochemistry, not for structures that you'd notice by eye. Vertebrates are all really extremely similar at the genetic level. We're not even that different from mushrooms in terms of the whole genetic tree of life. (We're much closer to mushrooms than to green plants!) Yeah, a bunch of the human genome has to do with the brain, but even there puffer fish aren't that different from certain members of the U.S. Supreme Court.
I think genes that are common among all animals are probably of the least interest - they are sort of like the "int main()" of the human genome, in that every program (here, a biological program) must have them.
I'm sure there's room for a variety of approaches. Some people may want to study the mouse genome because it's so similar to the human one. Some people may want to study the genes that humans have in common with yeast. It all depends on what you're trying to find out. Yeast doesn't get cystic fibrosis, but it might have some of the same cell-metabolism genes we do. If you can get the info you want from a "simple" organism, it may be easier.
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70% of all dna shared by most animals anyway? I mean, even between a human and say, a yeast....
is it really surprising that a puffer fish has a lot of the same genetic material?
Thalia
1 BASE = 2 bits. (CATG....four bases) Double that figure.
Of course, the use of the fugu as a comparative tool begs a fundamental question: Why does its genome have so much less junk than ours? And what's all the junk doing in genomes anyway?"
We humans have so much of junk along with some wonderful things; that's what makes us human and not Fugus.
There's always sufficient, but not always at the right place nor for the right folks.
most fugu that you get in Japan is farm raised and is not poisonous. It is also heavily government regulated, so there is absolutely no risk. This also has an affect on the flavor, the nonpoisonous fugu is bland and rather ordinary tasting. However, it is still possible to find the poisonous variety, though it can cost upwards of 1000USD for a plate.
The articles linked said that 50 people in Japan die from fugu, not the 1 or 2 that you claim. Still pretty safe.
:-)
As for regular sushi, it doesn't kill anyone. Sushi is very safe to eat, and it's extremely yummy. If I find a person who won't eat sushi, and has never tried it, then I feel very sorry for them. But what can I do if someone wants to die a virgin?
If tits were wings it'd be flying around.
Here is a link to the classic Simpsons episode, One Fish, Two Fish, Blowfish, Blue Fish. Homer eats poisonous puffer fish and he thinks he has only 24 hours to live.
--------
Oscarfish.com: tropical fish with attitude. Way t
I'm sorry, by posting this transcript, you have violated the Intellectual Property rights of the Simpson's owners. They'll be hauling you into court any day now.
[W]henever researchers have gone into the fugu and looked for human genes, by and large they've found them.
But only if they look in the right Plaice
the link saying very short genome is the story
"Cornflakes are not the innocent critters they seem"- Sterling Morrison
scientests)
The "Junk DNA" refered to in the article is actually called non-coding DNA. This 95% of the human genome switches the 5% of DNA that actually codes for chemicals. Its like if you bought a one-hundred page book, and you opened it to find 95 pages of instructions on how to read the 5 page book that followed.
Thats the analogy my biology teacher used I personally think that its a crappy analogy, but i cant really think of anything better.
- EnDough
It all goes back about a million years.
Urg the caveman stepped on one of these fish, got pissed off, and said, "blow me". The rest is history.
Well,
it's all down to entropy. A shorter gene sequence might have its uses (less energy to copy?) but redundancy is king when you have a high error rate for the copying. I would imagine that DNA has evolved to be highly robust in the face of mutation, which is in direct conflict with reducing representation size.
What would be really cool would be to work in some industrial strength error correction code into the copying mechanism (grey codes for example). If we are to go into high-radiation environments such as space, some sort of additional error correction will likely be needed in our genes.
does anyone know whether representation plays into gene interpretation? Ie the physical folding of the protein interacting with how the data it holds is interpreted (visualise paper tape which holds not only printed data, but is also knotted in such a way to expose some letters and obscure others).
ObIANAGeneticScientist
Gee, if only the human Genome was commented...then we'd have no trouble at all understanding it. If only God commented his code...then as a collective species we'd pull an M$ and ruin it for everyone. If microsoft made humans...ewwww I don't even want to think about that!!!
So if the genes are almost the same then wouldn't eating it make one a cannibal? I eat human flesh normally so I have no problem with this but I know most are opposed to it on moral grounds.
Just remember... you're not really studying the mice. They're conducting incredibly subtle experiments on YOU.
End of lesson. You may press the button.
...then Bill Gates would be able to fullfill his dream of Windows Everywhere(tm)--imagine the horror of replacing GOS (God's OS) with Windows For Your Brain.
"Excuse me, my brain just ran out of system resources. Please wait a minute while I reboot..."
Liver, gonads, intestines and skin. (You could have read the provided FDA link, you know.)
There are fugu restaurants in Japan, where the thrill of risking death by eating even a slightly tainted sliver of meat is the whole point of the experience.
Yup. In fact, the more expensive the fugu part, the closer it is to the poisonous organs (and the greater the risk of dying!). Connoisseurs say you actually get a buzz from fugu with a tiny bit of poison in it...
You must be a licensed fugu chef to work at such a restaurant, but there are a number of "black market" fugu stands around, too.
This, on the other hand, is bunk. Any restaurant that tries to sell fugu without a licence would instantly get slammed by Japan's Health Ministry, as would any "stall" that tried to sell any type of raw fish. However, you're free to go fish your own fugu and serve it up to your family, and this is in fact the reason behind most of Japan's fugu deaths.
Michael T. Itamura refers the interested reader to the August 1984 issue of National Geographic. Stories and photographs of the leopard puffer. (Even a story about a famed Kabuki actor who ate the liver of the puffer and paid for it with his life).
Matsugoro Bando... XIV? Can't remember. Anyway, he wasn't quite stupid enough to eat an actual poison organ, but he did bribe a chef to give him a piece usually deemed inedible due to its proximity.
Incidentally, I'll be going to eat a fugu dinner next week...
Cheers,
-j.
No, because you only need one of the pair to determine its partner. DNA bases pair up predictably: A with T, G with C. So if you have a sequence of bases
CATGATACAGTAG
then you know the respective complements will be
GTACTATGTCATC
so you only need two bits per base pair to store the data. (Disclaimer: I haven't studied biology since high school, so I could be misremembering.)
I wonder what the genetic analog of gzip would be...
--
BACKNEXTFINISHCANCEL
Apparently that was one of the reasons for the great debate obver the ethics of exterminating the virus.
'There is a Light that never goes out.'
anyway enough ethics, most don't seem to think ethics is relative to science anyway (except for SF writers, and a few truly smart people),... here's a more practical and useful opinion:
next time you are in Osaka make sure to try Fugu Shabu Shabu.... mmmmm, the best meal i've ever had
Hmmm, I though sushi was quite healthy actually,I've been told that you should freeze the fish for 1 - 2 days b4 eating it in order to kill off some possible parasite/germ/something, after that it should be no trouble eating it... ;-)
Heard though that the s. koreans got one of the highest rate of stomach cancer because of their habit of eating kim-shi (sort of pickled cabbage) al the time... THing is, I understands them.... it's food of the gods!!
It is wicked food though
if (!signature) { throw std::runtime_error("No sig!"); }
mind you, it's not software installation.. It's (ummm) AI!!! *Learning software*!!! wow!
Also, after the boot, you rarely find a need to reboot, only when there's a hardware failure. Remarkable stable, no reboots, just sleep!
mind you, it doesn't do well to leave it switched of too long in case of a crash.. reboot will be needed as soon as possible (approx. 5 min. longer if cooled down), otherwise refusal to reboot or data corruption might occur...
oh dear.. bit off topic today..
if (!signature) { throw std::runtime_error("No sig!"); }
Only 5 percent of human DNA is useful and the other 95 percent is wasted? Maybe thats why people like beer so much.
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If the puffer fish contained all the human genes, then by and large, the puffer fish would seem awfully human. But it doesn't. Its even got extra stuff, like gills and chemicals that are cardiotoxic
Actually the human embryo does have gills during a portion of development. If I remember my cell bio correctly, only about 1% of genes in the human genome are expressed at any one time, and most are never expressed.
Now, to the best of my knowledge, no killer bacterial strains have yet shown up in fish, so you're probably pretty safe. But, one day something like samonella or mad cow disease could show up in salmon, and then say bye bye to sushi. Until then, the worst you're likely to suffer is an upset stomach.
"The question of whether a computer can think is no more interesting than that of whether a submarine can swim" -EWD
Damn, thats ironic. That episode was on last night on the local Fox station.
Hmm, so if puffer fish share certain generic genomes in common with humans, could they be used at some distant future date to "fill in the gaps" for reconstructing ancient human genes entombed in amber-cased gnats? Sorta like they did with frog genes in Jurassic Park?
My, that would be a rather lame adventure park, "Cenozoic Park," even sans Richard Attenborough. I would demand my money back.
(...biologist)
But I have to say I'm suprised at the number of people posting who think "puffer fish are so different from humans"
Let me remind you of a fair number of similarities...bilateral symmetry, two eyes, fins vs. arms, spine, oxygen/co2 exchange is somewhat similar as I recall.
I've always thought most animals are quite similar. Not as much as say, bonobos and humans, which are some 97% genetically identical, if memory serves, but most animals share a number of basic traits that are probably nearly identical in the genome coding.
plus i've heard a lot of a given animals genetic makeup is dormant garbage left over from ages of evolution. In that case, there could well be a puffer hidden in all of us (and not via the sushi method)
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My girlfriend's folks have a fugu restaurant in Tokyo, and it's really not as bad as it seems. Everything is regulated pretty well, and it takes a *long* time to become qualified (>5 years full time training/practice IIRC).
Better to stay silent, and let people think you're an idiot than to open your mouth and remove all doubt
true - however, i believe most of these "human" patents are done in such a way that the owners already have a spanning reach in this area. i.e. they can claim patents now not only on the "human" genes, etc. but those of the fugazi or whatever the hell it's called again (puffer fish).
anyone wanna hear my rant on why intellectual property is bad again?????? anyone????
FluX
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"It is seldom that liberty of any kind is lost all at once." -David Hume
Actually, couldn't you do an encoding in 2 bits?
1 bit - A/T (set), C/G (unset)
1 bit - first base + strand (set), first base - strand (unset)
Thus,
5' ATCGATCG 3'
3' TAGCTAGC 5'
becomes:
1110010011100100
('course, you have to make an assumption as to which strand is +, and what the "order" of a base pair is (A/T or T/A?)...)
Interesting...
Let's try not to let fact interfere with our speculation here, OK?
Let me tell you how it all started:
In The Beginning
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%Create fish
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#And God saw man and woman being fruitful and multiplying in Garden.edn
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#Done
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#Warning system error in sector E95. Man and woman not in Garden.edn.
#1 errors.
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- if you love something, set it free; if it doesn't come back, hunt it down and kill it
nevermind...somehow i thought you said *3* bits originally...=)
Let's try not to let fact interfere with our speculation here, OK?
Obviously, the Puffer fish is going to have many genes that a human being doesn't, however, the vast majority of genes are going to be, at the very least, homologous. A person "shares" 50% of her genes with a banana; i.e. the genes are present in homologous form.
Recall, human beings have gills for a significant period of time. Whatever genes encode for the signals that causes gills to form - and that is the way it works, genes encode chemicals, there is no gene for gills - are present in a person, and if we can find them in a puffer fish it becomes much, much easier to locate them in a human genome. Furthermore, once we know what the genes that make the signals that end up forming gills are - it becomes easier to find the (presumably similar) genes that signal for hair, fingernails, lungs and so on.
Finally, the Genes that are in a person and not in a puffer are probably NOT the point of real interest in the human genome. The big differnce between a human being and a puffer is not in what genes are actually present, but in 1. sequence differences between homologous genes in the puffer and in a person, and 2. in differences between activity (transcriptional frequency) of homologous genes. It is this difference in the rate at which a particular gene is transcribed (which can, in some cases, be traced to a totally different gene, but I digress) which cause you to no longer have gills like you did when you were -1/2 years old.
The fundamental stuff - the stuff that both a human and a fugu have in common - is still nothing like fully understood. The analogy to the main fxn of a c-program is invalid; the developmental genes are more like the symbol table of the c-compiler, which is the first thing you'd want to take apart if you wanted to reverse-engineer how c works from some very poorly commented code.
Dr.Praetorious
UCSC Molecular Biology
My suspicion would be that after the human, mouse & fugu are finalized that the next genome to sequenced will be the Chimpanzee. Then the question is -- what genomes do you sequence after those? I've argued that since aging is the disease that everyone has, that genomes of non- or slowly aging organisms would provide a great deal of information about what improvements need to be made to the human genome to allow us to live indefinately (longvity limited by our accident rates). The genomes that would provide interesting insights include elephants, whales, tortises, lobsters, giant clams, bats and parrots or maccaws. The genomes of all of these species have been tuned for extended longevity, perhaps in quite different ways. The genomes of species such as geckos, starfish, crabs and other animals that have the ability to regrow limbs would provide us with information on how nature has organized genetic programs to regrow complex tissues (something humans lack). Those who would like to push the NIH in this direction should send letters about this to the Office of the Director of the NHCGR. See this link.
For those interested, I maintain a page with a semi-current status of many of the genome projects here.
Ok, I'll grant you that, but like you said... we're a few billion years behind the game :-)
"I may not have morals, but I have standards."
"I may not have morals, but I have standards."
The human genome has a lot of things in it called "Introns." They are, in a terrible analogy, like comments in code. Like comments, they *may* have subtle effects on who uses the code - the mRNA (which is what the gene turns into on it's way to becoming a protein) spends a while with the Introns still in it, and these Introns may have some effect on the frequency or likelihood of the mRNA in question eventually being used to make proteins. Vast oversimplification, of course. "Lower" organisms also do something called "alternative splicing" with their introns, where you occasionally skip the coding region inbetween two introns, and thus the same gene ends up leading to two different mRNAs with some frequency.
The genes which are "found" in fugu are found by homology - in particular, they run the human gene and the fugu gene sequences through some sort of state machine with weighted transitions (it's the same technology that the first voice recognition stuff uses, if any of you do that) - if the total weight of the transitions in the best possible traversal (this is determined by some kind of dyanmic algorithm the name of which I cannot remember) is below a certain amount, it means (and yes, it really does mean this) that thet two genes are evolutionarily related. The name of the engine in question, which searches a database for genes that score high on this sort of test, is BLAST.
This may or may not mean that the genes code for proteins with similar functions - it probably does, but you can't say for certain.
Dr. Preatorious
UCSC Biology
Eh... not really. More like it's part of the body of the program. I don't really like the whole "Genome == Computer Program" analogy because in a lot of ways they're very different animals, or at least the way we code is not the same as the way nature codes.
The crap, if it's anything, is more likely something that has a lot of different functions in development, from breaking up functional genes to providing a reservoir for new genes, as well as influencing an organism's development or differentiation.
Remember, if you want to think of the genome as a program, think of it as an infinitely recursive, self-modifying one, and you get to realizing just how unlike any program it is.
"I may not have morals, but I have standards."
"I may not have morals, but I have standards."
Firstly, it's _not_all that much information. 1 mega-base = 2 mega-bytes; DNA only comes in A,C,T and G.
The search enginge that makes it possible for scientists around the world to coorelate this sort of data is called BLAST:
http://www.ncbi.nlm.nih.gov/BLAST/
If you poke around the web-site for a while, somebody has probably come up with something better than BLAST while I wasn't paying attention.
I really should learn html. Anybody recommend a particular book (as opposed to the doznes of others, not just one that you happen to know exists.)
Dr. Praetorious
UCSC Molecular Biology
A friend at college who was a geneticist told me he worked a lot on muntjack deer. Apparently they have "nice, big chromosomes".
This was before he gave up drinking, though, so take this information under advisement.
Yes. It has the color of hamachi, just a bit paler. And it usually is cut to much thinner pieces than other sashimi.
Looks like fresh eel meat at the first sight. But the texture is between that of the eel and the salmon.
Overall it tastes good. I recommend having it once, in a famous restaurant in Japan. Fugu poisoning only kills about 100 people a year.
Also there's an alternative type of fugu or so I've heard, cultivated not caught. And is much less poisonous. I'm not sure about that tho.
It's simply unAmerican to threaten the country's moral fiber by tearing down the Olympic pantheon's primacy.
To avoid getting eaten?
-=-
"Everything you know is wrong. (And stupid.)"
Moderation Totals: Wrong=2, Stupid=3, Total=5.
telomeres: lengthyish non-coding reigons of DNA at the ends of chromosomes with an uncharacterized structure (several models exist) which is thought to assist in DNA replication which are widely thought to be shortened through replication (although possibly not in cancerous/other rapidly-dividing cells).
Your average somatic, non-epithelial/neural cell divides every 7 to 10 years or so unless there is some kind of damage, and AFAICT, this research has little to nothing to do with telomeres, or making anything longer.
Also, do the human-fugu match up genes play similar roles in each species?
As other posters have stated, highly conserved genes which have simmilar/identical biochemical roles will be very similar in sequence between the fish and humans.
There are 1.1... kinds of people.
Check out geneontology.org for more on a project, still in its comparative infancy, which aims to bring all of this together.
The best newspaper in the USA: the Anderson Valley Advertiser.
Actually, it wouldn't be all that difficult to fit a human being onto a cd, as much of the human genome is repetitious and boring (read no genes).
Just gz humangenome.bin
Don Armstrong -".naidnE elttiL etah I"
http://www.donarmstrong.com
Anyone else notice that it looks like more the "more evolved" specicies have less base pairs?
Is this just the result of my pre-Coperican biases? Or some observational bias that they wouldn't have printed numbers for small spieces?
Does anyone know if this pattern I've inferred holds true with a larger database of species?
The best newspaper in the USA: the Anderson Valley Advertiser.
the ultimate prior art attack. =)
My .02,
My .02,
zencode
iactivist.org/jason
But who gives a crap about a *normal* Na+ channel? The promise of genomics is the elimination of things like Cystic Fibrosis and Sickle Cell Anemia. These disorders are pretty specific to humans, so it makes no sense to go mucking about in some other animal's genome to cure them.
Back to my programming analogy: all these genes that are common to many animals, well we need to learn about these, but I don't see much useful coming from it. These genes are sort of like a C reference manual - tons of information, no utility. But genes that code for CF or SCA or cancer - these are more like the Linux Source code - written in C, but much more practical, and much more useful.
Albert Einstein once said that nature is as complex as it needs to be, and no more. True, only something like 3% of our genome determines phenotypical stuff (height, hair color), but I think that as the genome mystery is unraveled, we will begin to see that our genome isn't just an important 3% bundled in 97% of crap. If it were, I think nature would have naturally selected out those humans with an inefficient DNA long ago. I think the 97% that is considered unimportant now will likely be found to be vital to protein expression, apoptosis, and things we haven't even thought of yet.
you're missing a big point (5) when doing comparitive genomic analysis it's very very helpful to have organisms that are very differen yet conatain the same genes. It really make the controller regions for a gene stick out like sore thumbs as they remain conserved across genomes yet don't show up on any gene prediction programs. This is a very nice shortcut to understanding how to turn genes on and off.
check out more on fugu sequencing at our website doe fugu sequencing
Only about an average of 1 or 2 people per year die in Japan from eating improperly prepared fugu, and all of these are from those black market places. More than that number of Japanese people probably die just from the fact that they're eating raw fish all the time :)
"The question of whether a computer can think is no more interesting than that of whether a submarine can swim" -EWD
errgggg... the better link is
Fugu
Although usually you die within 15 minutes of consuming the fugu if prepared incorrectly, if the toxin is in a small enough dose, your heart and breathing rate will slow down as to be undectable for a few hours to a few days, and then you recover. There was a movie about this, some stupid thing, but suprisingly accurate of their portrayal of the effects of a minute amount of tetradotoxin.
/.'ers.
Also, in some islands where exists the zombie cults (where the zombie idea originated), they have what's known as "zombie potion". This, among other weird ingredients contains puffer fish, which can (don't know ho often tho) result in the person "dying", and then "coming back to life" a day or two later, and believing themselves to be zombies, and under the power of the shaman who created them.
Bet ya'll didn't know that! Unless of course it's on the links, I didn't bother to read 'em, like most
--Gfunk
Send lawyers, guns, and money!
More info on Homer's close brush with death can be obtained from the transcript of this episode of The Simpsons.
What would be really cool would be to work in some industrial strength error correction code into the copying mechanism (grey codes for example).
DNA replication is already good to 1 error in 10**9 bases duplicated. Assuming I haven't screwed my numbers up completely, that's about 3 single base pair errors per complete duplication of the genome. That's pretty damn good. What's more of a problem is DNA repair, which is somewhat less efficient (not just because it makes mistakes, but also because sometimes information has been completely lost). Some sort of checksumming would be nice, but it's not something you can retrofit without changing the entire biology of the cell.
Note that this wouldn't necessarily be a good thing - reducing mutation is probably good for the survival of individuals, but not necessarily for the long-term good of the species. Mind you, by the time we've reached sufficiently advanced technology to be able to cope with a project that size we'd probably be able to "enhance" genes somewhat more accurately than random changes.
does anyone know whether representation plays into gene interpretation? Ie the physical folding of the protein interacting with how the data it holds is interpreted (visualise paper tape which holds not only printed data, but is also knotted in such a way to expose some letters and obscure others).
I assume you mean DNA rather than protein? If so, yup. In its default state, DNA is tightly wound around a protein scaffold and can't be transcribed into RNA. Whether or not the DNA is in this inaccessible form depends to some extent on the sequence of the non-coding DNA around it amongst a variety of other things.
Thats the analogy my biology teacher used I personally think that its a crappy analogy, but i cant really think of anything better.
It's also not terribly accurate. Some of the non-coding DNA is involved in controlling gene activity, but large chunks really do seem to be, well, junk. Removing small chunks of non-coding DNA is unlikely to be enough of an advantage to give you a significantly better survival chance, and removing large chunks is difficult without also removing coding genes.
A couple of comments on this:
First, when people talk about genetic similarity between species, they're generally doing fairly meaningless things like looking at sequences of coding regions of certain genes (the parts that get transcribed and made into protein). This is pretty meaningless for a couple of reasons: first, sequence similarity does not correlate 100% with similarity at the protein level. The dolphin hemoglobin gene might have greater sequence homology to the human gene than mouse hemoglobin (it probably doesn't, but it could), but one could most likely replace every hemoglobin molecule in a human body with mouse hemoglobin with no problem. Dolphin hemoglobin, OTOH, has different O2 and CO2 binding characteristics, and would probably kill the person if the switch were made.
The more important thing to note, however, is that real differences in species are primarily due to different patterns of gene expression rather than different sequences in the coding regions of the genes. When you think about it, the difference between a human and a puffer fish is way beyond the genetic level, anyway. Fibroblasts or white blood cells from either species would look the same growing in a dish--it's the organization of the cells into tissues, the tissues into organs, etc. that makes the difference. If someone's sequencing the fugu genome, it's probably not because the fish is so similar to humans, but because the fish is cheap and easy to work with in a certain experimental preparation.
Sushi is the safest when the fish is fresh. I mean fresh. The longer a piece of fish sits around, the more likely it is to pick up something from the environment that will contaminate it. As for freezing, eeewwww. Sushi is also best when it is fresh. The freezing would destroy the consistancy of the seafood, which is one of the crucial parts to a good meal.
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What's worse, you can't know what you think you know, no matter how hard you try.
If you haven't read it, try Godel, Escher, Bach, by Hofsteader (sp?). Excellent book.
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If the junk is a place holder, then it may work the same as the things like counters. The way DNA work requires more state info to be keep than current theorys explan.
Check out the table at the bottom of the article that gives some examples of the genome lengths of various organisms. Plants have longer genomes.
Is it possible that the amount of "junk" as they call it, could grow linearly with the number of times the genome is copied? If this were true, the length of a genome could be related to a revision number.
Hi, I'm a homo sapian (Life major version 23432 minor version 3.4 Billion). Available for download life-23432.3400000000(3.4 Gb). (I just made up the 23432 number)
Of course I know next to nothing about genetics, and it seems all too simple, but it's comforting to make very complex things seem simple.
XJS*C4JDBQADN1.NSBN3*2IDNEN*GTUBE-STANDARD-ANTI-U
It seems to me if we are finding human genes inside puffer fishes, it may be due to their diet :)
It would be a shame to cut up something so cute :)
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is you support biology topics because you're a kharma whoring bastard?
I guess I should thank you for responding, and letting me bring up yet another problem with slashdot besides the three useless staffers (michael, timothy, katz), and that is the oh-so-great practice of kharma whoring. I'm sick of seeing fifty anonymous posts for every ten posts with names because people are afraid they'll lose their precious kharma. It's pathetic; it leads to a practice of overly-cautious and self-conscious posting, which limits actual valid conversation. I want to point out, for all of you who think I'm talking out of my ass, that this is my third consecutive post that 99% of all readers would have posted anonymously, with no fear at all attached, because kharma is not something that should be bargained for, it should be a fortunate side effect and nothing more. If your whole goal is to see "+5, informative" show up next to your post, type it into your bio, or make it your email address. Otherwise, post because you have something to say, not because you want recognition for what you have done.
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The average length of a human coding sequence in the DNA databases is approximately 1.2 Kbp and sensible estimates of the total number of genes in the human genome lie between 50 and 100,000. A gene number of 70,000 would give a total coding sequence of 85 Megabases, less than 3% of our genome. Herein lies one of the major problems. A 3% return on investment, even when genes are identifiable, is rather poor, especially when sequencing is an expensive business. As if that's not enough, a large percentage of highly re-iterated dispersed repeats serve to exacerbate the problem. The average length of a human coding sequence in the DNA databases is approximately 1.2 Kbp and sensible estimates of the total number of genes in the human genome lie between 50 and 100,000. A gene number of 70,000 would give a total coding sequence of 85 Megabases, less than 3% of our genome. Herein lies one of the major problems. A 3% return on investment, even when genes are identifiable, is rather poor, especially when sequencing is an expensive business. As if that's not enough, a large percentage of highly re-iterated dispersed repeats serve to exacerbate the problem. Consequently other more direct approaches are being used, mostly to identify coding sequences within large genomic regions of DNA, and it is only by using a combination of these more elegant strategies that 'gene hunters' are able to operate economically. Some of these methods compare human sequences with sequences from other organisms, using the premise that conserved sequences have some function. An extension of this, particularly amongst mammals but also with chicken, is to identify conserved linkage groups, and this may have particular value in positional cloning projects. Conserved linkage, or conserved synteny, can in fact be used to great advantage in comparative genomics, particularly if a genome is smaller and easier to work with than the human genome.
When an article states that a fish has the same genes as humans, the meaning of 'the same' is best compared to: A rabbit has all 'the same' organs and limbs as a human: liver, heart ,lungs, skin, eyes, arms, feet etc.
Patenting genes is not about patenting a sequence of base pairs. A bit of DNA on its own just isn't useful. The interesting bit, is the protein the gene codes for. I'd be very much surprised if the fugu had any genes identical to their human equivalent.
"To truly understand biology you need a model organism" : mmmh you seems to be a scientist so use the term : genetic or biotechnology instead of biology because i dont'think you can even try to understand biology with a model organism...
I myself used to work on yeast and bacteria. And what i saw (not only in my work, lab, departement but in my read etc..) is that human being is trying to modify animal's genome to its proper use.
Bacteria is a good model because it's simple (expression of genome is directly the response to the cell environnement wich is not another cell but the external environnement). But it's really usefull because it produces our antibiotics, yeat produces 3 fundamental things (for a french i think ;) beer, bread, wine... bacterias produces a lot of chinese sauce, is useful for tea... so its good to make money !
and we're not trying to discover the mistery of life and stuff like that nonono, we're just learning how to make more money...
the first thing to proove that can be that nobody ask this simple question :
what's the non-coding genome for ?
coding genome (the gene) is almost all part of bacteria's genome, but it's only one percent of the human genome ? so why did we focus to the gene themselves ? maybe you can say that it's because we don't know now what's that for ??? but the really reason is that a few people, those who invest in research ask this question :
how can we have profit in learning this... I mean now not for my son !
that's it and if i can make a parallel with computer like you : research (biology oups in biotechnology of course !) is not interested by learning how to make a good system with free people that are trying to make it better and better for the human beiing in a all (like the gnu project for exemple). Research is interested by making a lot of money and controlling you're knowledge, your aim, your langage, by one little buggy system and suite of program... like whom ? i let you find it :)
and when i said research : i don't say scientist but the one who control the science, the big investor !
Actually, the process you describe is very advanced and does make human coders look shitty. Otherwise, why do't they use the same model? It's just to complicated and took several years (some bilion and change) to develop, but it's by farv the most code-effective way of making something happen!
Sig (appended to the end of comments I post, 54 chars)
See http://neuroscience.about.com/science/neuroscience /library/weekly/aa000619Zombie.htm
And you thought they were just processes without parents!.
Old COBOL programmers never die. They just code in C.
This is not a Fugazi
I think a more likely reason that "by and large, when we've looked for human genes in the puffer, we've found them" is that we currently know about only a few of the important genes in the genome - we've just scratched the surface. Perhaps now we should try to find genes in the human genome that are NOT in the puffer, and then see what THEY do. I think genes that are common among all animals are probably of the least interest - they are sort of like the "int main()" of the human genome, in that every program (here, a biological program) must have them.
It is fugu, a blow fish, that has the deadly nerve toxin in one of the internal organs (either the liver of gall bladder, I forget which). There are fugu restaurants in Japan, where the thrill of risking death by eating even a slightly tainted sliver of meat is the whole point of the experience.
You must be a licensed fugu chef to work at such a restaurant, but there are a number of "black market" fugu stands around, too.
However, fugu usually kills you within 15 minutes, not 24 hours. It starts with a tingling in the fingers, and works its way up your arms and legs, until you are completely paralyzed, and you die when it reaches your heart.
I'd guess that the fugu chef, and the doctor, were having a little fun at Homer's expense.
Spage Yee {sy}: This fish is poisonous because its innards contain tetratodoxin (TTX) which is a neurotoxin, which blocks either the sodium or potassium (one or the other it's been a while since I studied neurobiology) channels in your nervous system.
Michael T. Itamura refers the interested reader to the August 1984 issue of National Geographic. Stories and photographs of the leopard puffer. (Even a story about a famed Kabuki actor who ate the liver of the puffer and paid for it with his life). Quite interesting.
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I'm actually watching tonight's episode (6:00p.m. where I live), 5F11, where the model UN gets stuck on the island - and Bart goes snorkeling to retrieve a cooler of food. There's a puffer fish waiting for him in the sunken school bus.
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Oscarfish.com: tropical fish with attitude. Way t
Oh look, we're all getting modded down. I love how these moderators work. I replied with a clear subject to a certain reply (not the parent article) and get modded down for asking a question. Then someone tries to answer it, and they get modded down. To hell with my karma. I really like slashdot, I like discussing in the forums. I like reading what everyone has to say about "breaking news", and I love the "back and forths" that take place. This kind of moderation kills that. I know that I am repeating what a lot of posters have been saying for a long time, but screw you moderators. Rather than bitch like sig_11 i think im just going to accept the fact that my karma is going to be near zero. I'm starting to realize that if something is put up for mass review on some website, like those popular self-photo rating websites, the more people that rate the material the lower rating the material will get. Thats the new slashdot effect. Disgruntled geeks who think their shit dont stink. im done now
hehe they played this episode today on fox, are simpsons creators slashdotters?
Well,I am not sure how useful this would be as far as locating disease causes and all is concerned, since humans are mammals and fish are aquatic creatures and I am sure that means a LOT of differences in the genes. Still, I think it might be a good idea to do it. Just curious here...anything like a complete genome for any organism, even this, means a LOT of information to be stored. I wonder how database applications would cope with this kind of info. I read something about special research going on for information storage techniques for genomic databases, but as far as I remember, they addressed the needs for the genome of one particular organism only. It would be a nice reserach problem to see if it possible to correlate the data from various organisms for similar genes and see what yields, both in terms of information science and biology.
Did you hear about the mathematician who named his dog Cauchy because it left a residue at every pole?
So where's the human poison gene?
This learning software requires a lot of RAM and frankly, many people just don't have enough available to run this learning software at a decent speed. :P
Seriously though...
If the fugu has nearly all of the genes humans do, could this be a backdoor around patents related to the human genome?
Devide by 1024*1024 == 95 Mbytes.
...
"You are the product of a mutational union of ~640Mbytes of genetic information."
You contradict yourself.
Zahlman Q. Namlhaz, esq. {:> "Zahl Incorporated - the Last Word in Everything(TM)"
ugh. never again.
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Shhhhh....there's a dead body in my trunk.
Wanna see it? Fuck around and you'll be it!
_____________
this is a sig
That's an interesting idea, but I'd think it's more like offsets to allow correct (or incorrect) modification. But, like I said... it's not really like a program because it's got very different limitations than a computer. You can have infinite recursiveness (i.e. infinite memory) which changes the whole game entirely.
"I may not have morals, but I have standards."
"I may not have morals, but I have standards."
Just wait until Rambus sues us all for patent infringment......
Seriosly, cna't remember, but think I read somewhere that all the input a human takes in during her lifetime is about 20- 40 GB or am I completely out of track here? Basically our brain dumps most of te input and just generalize after models, like when we see a human, we already know it got 2 arms, 2 legs
face, etc, etc...We know the normal behaiour, etc.. that's why people in really streesed or out-of-order situation can have a hard time rmembering what actually happened. Saw a program about the brain and there took a bank robbery as an example. People couldn't tell who's been waiving a gun or how many ppl who did that. cause that's not part of our model of everyday life. So the brain actually has to try to keep up realtime with what's happening, which it apparently do quite poorly...
Anyone who know more...
umm, sorry, this is going *way* offtopic!!!
OSrry moderators! *smile*
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That's very true, but that doesn't mean this can't be used. One thing that is very useful that I'd imagine, is to do experiments on the "junk" (my professors always called it "crap", a far mor elegant term in my opinion). I think that the crap could play a major role in the development of an organism, since the genes are pretty much the same in a lot of organisms (i.e. mouse to human to chimp etc.) but they wind up being very very different animals. It's not just having the genes that counts, it's how they are expressed from the start, and when you look at what's different in those embryos, it's the crap in the genome. Why not start throwing some human genome junk (large repeating sequences with no stop codons would be a good start) in to an egg and see what happens? Bet you it won't be the same old Fugu...
"I may not have morals, but I have standards."
"I may not have morals, but I have standards."
Human coders aren't shitty, they're just not working the same model. Human coders spell out every little detail of their system to get it to work right. The gene doesn't do that. It spells out the code of proteins, but it doesn't really say how they interact. It's tough for me to really explain this, but genes aren't like source code at all. It's kind of like having a bunch of diseparate functions (i.e. each gene) where the actual body of the program writes itself perpetually. Weird, huh?
"I may not have morals, but I have standards."
"I may not have morals, but I have standards."
The reason only 3 to 5 percent of DNA strands represent actual instructions is that genetics is basically an object-oriented system. You need some little protein that's been subclassed a hundred thousand times already, and presto! Gene bloat.
Someday they'll map the whole thing to C++ or Java; then you'll see why there's so much worthless code in your genes.
Telomeres aren't a gene, they're a structure.
The lengthening of the human genome? I don't think it's really lengthening any more than it's shortening (i.e. it's static due to deletions as well as insertions). It's just full of a lot of junk that doesn't get encoded. That may or may not mean anything on the whole, but who knows?
"I may not have morals, but I have standards."
"I may not have morals, but I have standards."
The original article that started all of this is a bit misleading; the relevant point isn't that the pufferfish is extra-ordinarily similar to humans. In fact, Fugu's genome is as similar to humans as one would expect for its phylogenetic position! The neat thing is that its lineage has lost large amounts of non-coding DNA, leaving 'just genes'. This is convenient because a big problem in comparative genomics is trying to just identify the genes. If we have a vertebrate genomic sequence that is fully annotated (ie. where all genes have been identified), this can be used as a reference point for studying the architecture and evolution of the human genome. Additionally, assembly of all the sequenced fragments of the human genome is generally quite difficult because much of the 'junk DNA' is made up of repetitive elements, leading to many possible overlapping contiguous sequences. Fugu has no repetitive sequeneces to speak of, so assembly is straightforward. Thats it. Yes humans may have lost some genes and gained some relative to Fugu--and yes, these will be involved in making humans human, or making Fugu Fugu. In this respect the common genes are boring. However, the main point is that Fugu is a vertebrate--and vertebrates are all quite similar physiologically, biochemically, and therefore genomically. As a final note, more DNA doesn't necessarily mean 'more information' if large parts of the sequence are "junk", or don't do anything. Contrariwise, elements of the so-called 'junk DNA' have been shown to play a role in affecting gene-expression (since they can contain transcription-factor binding sites)..and it is differences in gene-expression levels that are thought to frequently be responsible for the sorts of morphological differences that lead to ecological adaptation, and perhaps even speciation. In this respect, "junk DNA" can be more important than the actual genes--which is quite contrary to most people's intuition. This is more or less a modern incarnation of King and Wilson's "regulatory hypothesis" which suggests that humans are so morphologically and behaviourally different from chimps because of differences in gene-expression (though we are ~99% similar when it comes to our *gene* sequences).
The idea that a compact genome could be used to look for genes (or at least exons) in the human genome has already been put into practice. If you go to http://kicy.genoscope.cns.fr/cgi-bin/exofish_kicy. cgi you will get a short introduction on the topic as well as have access to the interface allowing you to look for exons in a sequence that you input.
EXOFISH (Exon Finding by Sequence Homology) uses DNA from another fish which is a cousin of Fugu (Tetraodon nigroviridis) in order to find highly conserved regions between it and human sequences. A method was developed to find these evolutionary conserved regions (ecores) efficiently as it is believed that they represent exons. More info here.
That wasn't meant as a jab against sushi. I like sushi too. I happen to prefer kappa, ebi and California rolls, none of which contain raw fish, but still, that's just a matter of personal taste. I was merely observing that they, the Japanese, eat plenty of other foods that are probably just as dangerous as fugu. For that matter, rare hamburgers can have bacterial infestations too (steaks just need to be cooked on the outside, but ground meat has to be cooked all the way through).
"The question of whether a computer can think is no more interesting than that of whether a submarine can swim" -EWD
"Of the 3.4 billion chemical building blocks that make up the human DNA strand, scientists believe only 3 to 5 percent represent actual instructions that make some people tall, some blue-eyed and some prone to heart disease. The other 95 percent of the human genome has been dubbed "junk" DNA.
I bet the junk genes spend their time soliciting porn sites, penny stocks, and get rich quick schemes.
I am not a geneticist
What I would like to know is:
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.
The answer is probably 42.
134340: I am not a number. I am a free planet!
How exciting!
By studying the blowfish genome we might learn why some men and women "puff up" so quickly just after getting married.
Dr. Hibbert: You have twenty-four hours to live.
Homer: Twenty-four hours!
Dr. Hibbert: Well, twenty-two. I'm sorry I kept you waiting so long.
Dr. Hibbert: Well, if there's one consolation, it's that you will feel no pain at all until some time tomorrow evening, when your heart suddenly explodes.
Dr. Hibbert: Now, a little death anxiety is normal. You can expect to go through five stages. The first is denial.
Homer: No way! Because I'm not dying!
Dr. Hibbert: The second is anger.
Homer: Why you little!
Dr. Hibbert: After that comes fear.
Homer: What's after fear? What's after fear?
Dr. Hibbert: Bargaining.
Homer: Doc, you gotta get me out of this! I'll make it worth your while!
Dr. Hibbert: Finally, acceptance.
Homer: Well, we all gotta go sometime.
Dr. Hibbert: Mr. Simpson, your progress astounds me.
400 million base pairs.
;)
1 base pair == 2 bits of digital information in binary.
800 million bits of information == 100 million bytes.
Devide by 1024*1024 == 95 Mbytes.
Make you realize how shitty human coders are in comparison..
To truly understand biology you need a model organism that is accessible experimentally. A good model system should have the following traits:
(1) Genetically tractable: basically this means that you can reliably perform matings and score marker genes for mapping.
(2) Easy to culture: can grow large numbers of the organism in a relatively short time for relatively little money.
(3) Easy to manipulate: have the ability to generate both random and targeted mutations, have vectors by which to insert transgenes.
(4) Easy to observe: simple organisms that have transluscent body walls are the best.
Fugu doesn't have ANY of these advantages except the small genome, so probably the most use that will come out of it will be as a reference organism. Experimentally, the best model organisms biologists have are:
(1) mice: best characterized mammalian model. you can do targeted mutations and insert transgenes, but random mutagenisis is hard. Histology and embryology is pretty well established, but mice like most mammals are very complex and often studies raise more questions than answer them. Genome sequence note quite complete yet, but getting there. :)
(2) fruit flies: Drosophila melanogaster is a great model system. The genome is relatively small (about 10^8 base pairs of DNA, and estimated 15,000 genes), but it has all the relavent organs and systems as mammals, and many genes function in the same way. Genome sequence has been completed.
(3) nematodes: Caenorhabditis elegans is also a great model system. Genome size is approx. the same as flies. Has the added advantage of having its entire cell lineage mapped. It only has 1000 or so cells, so it makes a super model organism for studying differentiation. Genome sequence is also complete. Disadvantages is due to divergence from the mammalian branch, it does some things oddly, so not quite as similiar to humans as flies are.
(4) yeast: the bug you use to brew beer, Saccharomyces cerevisiae. Single cell eukaryote, in fact the first eukaryote to have its genome completely sequenced. Great organism to work on really basic things like DNA replication and repair, and basic cell biology, but obviously not great if you are interested in Alzheimer's disease or hypertension. OTOH good for studying some kinds of cancers. You can grow a TON of yeast in the lab easily
(5) bacteria: Escherichia coli is ever simpler that yeast because it is a prokaryote, it has no nucleus. But it is good for stufying really basic mechanisms such as protein folding, translation, etc etc. You can grow 10 TONS of E. coli in the lab easily
Also, some ppl study Xenopus lavis (African bullfrogs), Danio rio (zebrafish), chickens, rats, among others, but by and large the major model organisms that are studied in a way relavent to medicine are flies, worms, and mice, and yeast and bacteria to a lesser extent. Often different investigators will collaborate with each other in a cross-species manner, and compare results between organisms to look for common themes in common problems.
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What does the lengthening of the human genome mean? I know about one gene called telomeres, in which a basepair gets shaved off during every replication as a cell divides and ages..
Also, do the human-fugu match up genes play similar roles in each species?
Goat sex free since 2001
What will they find if they go into human jeans looking for a fugu? And anyway, they say it's not the length of the genome that counts . . .
Sounds like a thorny issue...
<ducks>
Master, We need your skilled hands in the kitchen!
My skilled hands are busy!
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Society has traditionally always tried to find scapegoats for its problems. Well, here I am.
Well, I went to Japan in August, and happened to had some Fugu sashimi. It obviously didn't kill me, but it does not taste THAT better than other fish. I'd still prefer salmons. :)
In addition, there are processed dried fugus that isn't poisonous - but of course, it does not taste like the fish itself but rather like dried squid snack.
Talking about genome similarities here, why fugu but not any other simpler fish? I mean, the genome makeup of fugu must look more like that of an eel or a shark than....ur...humans.
Does it mean that it is the simplest fish in terms of genome complexity? Or is it the missing link? Just kidding about the second one...
I know what the junk DNA is... it's filled with first posts, links to goatse, and other viral troll phage sequences.
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man sig
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the pen is mightier then the sword. the sword is mightier then the court. the court is mightier then the pen.
in a class action suit, lawyers representing the fugu are set to argue that since they contain human genes, fugu are entitled to basic human rights. It is expected that the fugu will sue the Japanese government for 76 gigayen ($59 USD) claiming over 1000 years of abuse.
Arm yourself with knowledge.
Study which gene makes the fugu poisonous, h4x0r it with something else.
The day before we have GM fugu isn't far away - same great taste, without the risk!!