Slashdot Mirror
Human Gene Count Slashed
jd continues: "This has the potential for making life extremely interesting for genetic engineers, given that both individual genes and interactions between genes must be proportionately more complex, in order to get the same level of complexity out. Half the number of genes equates to twice the information encoded in forms other than discrete physical blocks of code.
There is no mention in the article of a story running in 2002 of genetic therapies unexpectedly causing cancer, although if you now factor in the increased complexity of interactions, it is possible that such side-effects can be better understood and therefore prevented. The new estimates, therefore, are more than just idle curiosity but have the potential for impacting how the science is approached."
Finally scientific proof that it's not the size that matters, it's how you use it.
That would be incorrect. The number of genomes in the human genome is 1.
Brandon
It is the number of genes that has been revised down. The genome is the complete set of DNA and contains all the genes.
The article poster mistook 'Genome' for 'Gene'. Organisms only have one genome as it is a collection of genes.
Go to the back of the class!
25,000 genes will be enough for everyone. - 2004
The new estimate, of between 20,000 to 25,000 genomes is marginally less than the 27,000 for the Arabidopsis, a flowering plant in the mustard family.
Damn elitist mustard, looking down on us.
In late breaking news, the final count of genomes in a typical human being has been found to be exactly 1. See http://en.wikipedia.org/wiki/Genome for details.
Where'd they off-shore the genes to?
"Like fire and fusion, government is a dangerous servant and a terrible master."~RAH
I think a good analogy for the /. croud would be ASM and C. ASM has a very small set of instructions and can be very complex to piece together. C has a much larger set and it is relatively easy to use.
The new estimate, of between 20,000 to 25,000 genomes is marginally less than the 27,000 for the Arabidopsis, a flowering plant in the mustard family. Earlier estimates had placed the number of genomes at around 44,000 - or even as high as 100,000.
AFAIK, there's a lot more research going into the human genome than into the Arabidopsis one. So one would naturally presume that the number of human genes would be known better.
But if the estimate for the number of human genes is subject to so much variation, how can you be so sure of that for the Arabidopsis?
Is this a meaningful comparison?
(Not to mention that the entire premise seems to be flawed..)
According to scientists, we gained 1000 genes compared to rodents when we diverged from them 75 millions years ago. And we 'lost' 33 genes compared to them (they have a functional copy, we have a nonfunctional pseudogene; it's still there, only not working - stop codons, etc).
The "we must have more gene than (insert stupid animal or plant here)" is funny. Our superiority complex at its best.
Read about the whole thing (with more links) on my blog (see sig)
Eureka Science News - automatically updated
This items made me recall a science film we watched when I was in grade 8. It was all about chromosomes.
There was an actor playing a typical I-don't-care-about-no-science-so- long-as-my-tractor-runs-right yokel who, as the 'scientist' (read: guy in a lab coat) noted that the fruit fly has five chromosomes and humans have 23, remarked "well, that's because people are the most advanced creatures on the planet."
The look on his face was priceless when he found out that potatoes have over forty.
I was at a lecture by Evelyn Fox Keller, and she said that there has been a paradigm shift and we're moving from breaking up biology into tiny parts, to seeing the whole picture. Whether theres 100,000 or 20,000 genomes seems rather trivial.
Science requires objectivity and dismissing ideas because they are offensive to your tastes is a bias. While intelligent design may not be probable, there is still a minute possibility that it could have occured. This needs to be investigated like anything else. Since it is unlikely, the priority should not be high, but the results should not be dismissed based on your political or theological views (and the results shouldn't be amplified for the same either).
Gauging the complexity is difficult, given there are a number of factors not currently understood, particularly the importance of non-coding RNA, which accounts for 98% of the genome. In the past, the information content of these regions was thought to be low, but this attitude is changing. As knowledge of the genome increases, the estimated number of genes drops, and more information emphasis is put on non-coding portions of the genome.
Evaluating the function of ncRNA is difficult because as of yet there are no statistically significant markers for them. Given the release today, and trends of late, more and more attention will be put on trying to decipher the utility of "junk" DNA.
Well, technically, you CAN buy genes. There are quite a few companies that sell pre-sequenced genes. In fact, the entire genomes of several organisms are available in varying amounts ligated into Bacterial Artificial Chromosomes (BACs) and plasmids. An interesting link is http://www.arabidopsis.org/ - There's a lot of information on Arabidopsis, where they keep a database of the entire Arabidopsis genome as well as many freely-available tools for its analysis.
to how many genomes are in a single human genome. However, speaking about genes in a genome, as the article states, this "correction" only counts those genes that make some discernable protein product. The number misses the number of open reading frames (ORF) that may not encode a protein at all, but a regulatory or enzymatic RNA. Probably, the next big project in life/medical research, after the big proteomics initiatives, will be the study of non-protein encoding ORFs. This problem is very tough to crack since 1) these RNA's do not have a common sequence element like "normal" messenger RNAs, 2) may be as short as 15 base pair (LIN12(?) in C. elegans), and 3) there are MANY, MANY possible ORFs in the genome.
Are these technically genes? They are regulated. They have a function. They are transcribed. The only thing different from the standard definition of a gene is that the RNA is not translated into protein.
In addition to multiple protein products from one "gene" as the article states, regulation of the gene may also be much more complex compared to "lower" organism. For example, the gene expression profile of the malarial parasite Plasmodium falciparum suggests very limited regulation. Basically, it looks like a linear progression with very limit amount of response. So, temporal and spatial regulation makes even multiple product genes seem to like a larger cohort of genes. Take the daughterless gene in Drosophila. It is used very early in embryonic development to control sexual differentiation. However, later, the gene product is used in neuronal differentiation. So, for the fly, sex is literally on the brain.
Actually last months Scientific American had a good article on this. Basically we are finding that what we once thought was junk (non coding areas and RNA coding areas which do not code for proteins) is probably some of the more important aspects of the nucleus. I quote:
"But investigators have since sequenced the genomes of diverse species, and it has become abundantly clear that to correlation between numbers of conventional genes and complexity truly is poor. The simple nematode worm Caenorhabditis elegans (made up of only about 1,000 cells) has about 19,000 protein-coding genes, almost 50 percent more than insects (13,500) and nearly as many as humans (around 25,000). Conversely, the relation between the amount of nonprotein-coding DNA sequences and organism complexity is more sonsistent.
There are 4 boxes to use in the defense of liberty: soap, ballot, jury, ammo. Use in that order. Starting now.
Only one? Ahem: Mitochondrial genome; Nuclear genome.
:)
As a mitochondrial researcher, I resent the most important organelle of the cell being overlooked or lumped in together with the nucleus here!
So I would say two genomes
Let look at that stats:
Terrorist kill ~ 3000 people in 2001 and it becomes a focus of the US nation. While:
Breast cancer kills > 40,000 / year
Prostate cancer kills > 30,000 / year
Diabetes kills > 70,000 / year
The numbers world wide of course are much larger.
Yeah OT I know but these kind of discoveries convince me our priorities are misplaced.
I've read the headline as "Human Genome Slashdotted" and I shouted: "Dear God, we're doomed!" My God, what an embarrassment... I need sleep.
Sincerely,
Pan Tarhei Hosé, PhD.
"Homo sum et cogito ergo odi profanum vulgus et libido."
I'm not sure how that is.
"We just have to get used to the fact that we don't have many more genes than a worm," Rubin said.
So how can humans be so complex with relatively few genes?
Seems to me like the instruction sets are the same, while the coding complexity varies?
Wow, my hat's off to you sir. That's the easiest 5, Informative I've ever seen someone pull off on this Internet or any of the Internets for that matter.
On the contrary, the complexity now increases. There are many genes that act in completely differen't roles depending on the cell type (nerve, epidermal, etc.). So a common language changes from cell type to cell type-- if one would even call it a common language. There is a large part of Bioinformatics/Computational Biology that deals with trying to determine interaction networks between genes. It's very complex, and difficult to deal with.
:) ).
With less genes we then expect to have a larger amount of downstream interactions between other genes. It might seem that with less genes then we have less to worry about, but we have already speculated for a long time that gene regulatory networks are complex.
To use an analogy (for all you computer geeks), it's like a programmer trying to read poorly modularized code. When you have no idea what class is doing what, and how they interact with other classes (as every class has multiple roles and talks to multiple other classes) then it is difficult to understand why the program behaves the way it does. If the program had many classes that were well modularized and designed with very distinct roles, then it would be easier to understand why things work the way they do.
With less genes and increased complexity we have an even more difficult task. It also highlights some of the reasons on why microarray analysis has not done what we expected it to do. Increasing the complexity and dependency between genes means that we probably are going to take a longer time understanding and extrapolating information from all these networks (which means more job security for me
An often unknown fact is that a single gene can code for thousands of different proteins. Protein regulation can occur in a variety of way, one of which is through "junk" DNA.
Currently little is known on the exact mechanism, which is a huge impediment to proteomics. As the phenomenon is elucidated, expect to see a lot more useful information coming out of genome projects.
Computationally predicting the 3-D structure and function of a gene is far more important than you probably realize. Reaching this point will revolutionize almost every aspect of your life, from pharmaceuticals, to nutrition, to silico-neural interfaces.
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Game: Player 'Donald J Trump' now has AI skill level 'experimental'.
To up the level of complexity, imagine that the blocks of code are randomly ordered (although blocks of genes tend to stay on the same chromosomes), are all executing in parallel, and can trigger reordering & rewriting of themselves & each other.
Yep, that's going to be one helluva debugger!
"The estimate for the number of genomes in human genetic code has been savagely revised downwards. The new estimate, of between 20,000 to 25,000 genomes..."
Only 20,000 to 25,000 genomes? I was sure that the number of genomes in human genetic code was closer to 6,500,000,000.
Sincerely,
Pan Tarhei Hosé, PhD.
"Homo sum et cogito ergo odi profanum vulgus et libido."
Actually, that's a bad analogy, since modern assembly possesses a significantly richer grammar than C. However, it is correct to say that the interactions between language elements (instructions) in ASM are very much simpler than in C.
More on topic: Why are people surprised that millions of years of evolution has resulted in a high entropy encoding "format" (the genome) whose consituent elements are multipurpose and have complex interactions with each other? An animal is more evolved (has a history of more complex environmental interactions) than a plant, so why shouldn't its genome be less redundant / contain more entropy? Comparisons of number of genes are (to return to the computing analogy) like comparing two processors based on their physical size.
D.
C'mon, it's trivial. Those are the comments in the code.
"sweet dreams are made of this..."
http://www.cogs.susx.ac.uk/users/adrianth/ascot/pa per/paper.html
Natural selection is not evolution. Natural selection is a reduction in the gene pool, not an extension. Useful genetic modifications are rare and hard to come by, not to mention they don't get passed on well. If you go and kill all white people, and only black people are left, evolution did not occur.
Gene count is a funny thing. Frogs, for example, have a lot of genes to guide their development from egg to tadpole to account for variations in water temperature and chemistry. Mammals gestate in a much more controlled environment (controlled temperature and chemistry), and hence do not need this huge complex of genes.
It's not wasting time, I'm educating myself.
This is definitely a mis-perception, usually based on the fact that most evolutionary descriptions only describe those things that lead up to humans. Plants are, in many cases, more highly evolved than animals are. Even than humans are. They just haven't specialized for intelligence.
It is a mistake to think that supremacy in one area (intelligence) means supremacy in all areas. Some people pride themselves on being efficient workers, others pride themselves on being paid well to do very little. In the biological world, plants would be the "blue pill" type of creature, the type B personalities, and they're REALLY REALLY good at it.
When I was working at Monsanto, I was told that wheat has a genetic strand about three times as long as the human genetic strand. This may or may not have relevance to the rest of the post, but I thought I'd toss it in just because it's interesting.
As another point, the length of the strand doesn't necessarily indicate a more evolved state. It can be assumed that some strands are more efficient than others, and thus don't NEED to be as long. Take Microsoft code, for instance. Just because they take more code to do the job doesn't mean it's a superior product.
Wake up - the future is arriving faster than you think.