Interesting post on the Celera thread about genes:
Message 13891225
Excerpt:
>>karljon wrote: "Here's another way of looking at it. Simple systems tend to have more stream-lined genomes. I know this is a gross generalization but,
for the sake of argument, it works. The genome of an amoeba is not as complex as that of the human."
So, in other words (I'm good at putting words in people's mouths!), let's hypothesize that there is a direct correlation between the complexity (or more
amusingly, the intelligence) of an organism and its genome size. Obviously this makes intuitive sense. We're bigger, smarter, and more complex than a
single-celled amoeba swimming around in its little pond. This is how science works: we hypothesize and then we test our hypothesis.
Here's some actual numbers on the size of various genomes for our little thought experiment (note these are approximations). You'll have to take my
word for it that this is not an exercise in data mining!
Species Genome size
Human 3,000,000,000 DNA basepairs (We all new that number!)
Cow 3,651,500,000 (Maybe your dinner was smarter than you thought? But at least it's a mammal like us.)
Chicken 1,200,000,000 (Pretty good for such a DUMB animal!)
Carp 1,700,000,000 (That makes sense. Carp are pretty dumb too.)
Zebrafish 1,900,000,000 (JD's favorite model, which CRA will sequence)
C. elegans 100,000,000 (The first fully sequence animal, an almost microscopic worm)
Fruit fly 180,000,000 (Well, obviously a fly is more complex than a worm with only 1000 cells. But wait, the big surprise is that CRA says the fly has
fewer genes than the worm, despite its greater complexity and larger genome. That's weird!)
House fly 900,000,000 (I guess that makes sense. At least it's bigger; probably smarter too. I still don't get that worm thing.)
Rice 400,000,000 (Insects and plants. Yeah, they're both pretty dumb.)
Tomato 655,000,000 (Yawn? Ever seen "Attack of the Killer Tomatoes"?)
Soybean 1,115,000,000 (Hmm?pretty smart plant. Almost a chicken's IQ. Must be all that inbreeding.)
E. coli 4,639,221 (Lives in our guts. Fully sequenced 2 years ago.)
HIV-1 9,750 (Given how nasty it is, I'd have thought it was bigger.)
OK, so what's the big deal? Most of that makes sense doesn't it? Well, here's a little more:
Warty newt 20,600,000,000 (I hate to tell you guys, but a Warty newt has a lot more DNA than you!)
Corn 5,000,000,000 (Even worse, so does corn!)
Paramecium A 8,600,000,000 (The one-celled denizen of pond scum from high school biology.)
Paramecium B 190,000,000 (Smaller? That's more like it! But they look the same to me.)
Onion 18,000,000,000 (The next time someone calls you a vegetable, take it as a complement!)
Salamander 81,300,000,000 (Damm!)
Lungfish 139,000,000,000 (What the hell's a lungfish?)
Fern 160,000,000,000 (I'm starting to get pissed!)
And the winner is:
Amoeba 670,000,000,000 (A mere 200X more DNA than your or I, all in one cell.)
Well, surprising as it sounds, the largest known genome is actually an amoeba!!! Great call karljon!!!
What does this all mean? It means that the size, complexity (and number of genes as I discuss below) has nothing to do with the size of the genome.
Now Sydney Brenner and the Pufferfish (that famous Japanese delicacy).
As I mentioned, Sydney is a living scientific god. JD will be interested to know that the C. elegans worm that biotechs like Exelexis and all those
academics perform functional genomics on was developed as a model organism single-handedly by SB. He was already a Nobel candidate prior to
this. He must be about 80 years old now, but for the last several years he has been championing the Pufferfish genome project. Why? Well not because
he likes sushi, but because Pufferfish have two interesting attributes. One, it's a vertebrate (has a spinal cord) like humans, and two, its genome is only
400 million basepairs long. Which as we now know is really TINY.
Well, besides being a really quick sequence for CRA, what's so interesting about that? Well for one, based on the sequencing that SB's done already,
Pufferfish have the same number of genes as human, give or take a few. Not just the same number, the same genes, period. After all, they're
vertebrates. So do mice and frogs and all the rest. They have most of the same organs as we do, and thanks to all the work done on Zebrafish (a
popular genetic model in academia), we know that most of their fundamental processes are very similar to ours. But yet they get by with only 1/8th the
amount of DNA we have! In fact, when SB sequences their DNA, what he finds is that pretty much all that remains are the genes and their regulatory
elements. That 6% or so plus some other stuff that we talked about above. Most of the "Junk DNA" is gone. But it's still a pretty happy little fish. [This
is why sequencing the Pufferfish is so important in SB's mind. Because its sequence is more diverged from human than mouse, and because all that's left
is the important stuff, a comparison between human and Pufferfish can be used to rapidly identify all those "regulatory elements" we were talking about.
The mouse, fly, worm, and Zebrafish can't do that.]<< |
