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Genome Surprise
Catskul writes "Along with the news that the polished and (more nearly) complete human genome being published Monday, comes a surprising observation about the genome: We have substantially fewer genes than expected; between 27,000 and 40,000 as compared to an original estimate of 140,000." Update: 04/14 01:22 GMT by T : For everyone who can't look at a Z, headline updated with an S in "surprise."
Ingredients
1 genome (preferably human)
4 eggs
1/4 cup flour
1/2 teaspoon baking powder
1-1/2 teaspoons dry mustard
1 cup cottage cheese
1 cup shredded Jack cheese
1 cup shredded cheddar cheese
3 chopped peeled green chiles
One 16-ounce package frozen hash browns
Shaker of paprika --dust top of casserole just before putting in oven - looks pretty.
Preheat oven to 325 degrees. Spray a small casserole dish with vegetable oil spray, 7 to 8 inches square or round. Line the pan with 1/2-inch layer of potatoes. Beat eggs. Add dry ingredients and beat well. Blend in remaining ingredients. Batter will be lumpy. Pour in dish and bake 25-30 minutes.
Serves 4.
Karma: Excellent Birds (mostly as a result of listening to Laurie Anderson)
We are simple creatures, no doubt. But the number of genomes does not point to our complexity. Rather, these genomes could be incredibly complex, controlling all sorts of things. They could intermingle, with no clear linear relationship between a single function and a single genome. It would have been easier to decode had there been more, because now it is clear that these genomes are more complex than originally thought.
Quid festinatio swallonis est aetherfuga inonusti?
Africus aut Europaeus?
This does not equal _gene expression_, or does not explain epigenetic effects.
This kind of news always makes me wary. Did the reporters mean what the author had in mind? Yes, when it comes to genetics I am more suspicious, after all, as a political tool it is too powerful for lunatics to be based on empty air; if you see what I mean.
Does this mean that we're all inbred? I think I'm going to log off and go play my banjo with uncle grandpa for awhile.
IAAL
Some of those oddities like tails are awfully curious to me. They're only somewhat inactive and are expressed in some people, and carry on down through their offspring - are they then really 'inactive' in the whole human scheme of things. ie some theoretical gene for "tail" or "no tail" for example, which is active would create a tail when present or not. But some fully inactive ones like "feathers" or "no feathers" which aren't used no matter what their state.
I'd see genes like those for a tail as being awfully rare, but not completely inactive
Now I don't know what the point of my post is. I think I wanted to talk about tails as I always wanted one when I was little. Instead I got some extra vertebrae, ribs, and a couple of mirrored organs.
I happen to like my monkey-like tail thank you very much!
Along with the news... comes a suprising observation about the genome: We have substantially fewer genes than expected
This observation was already made a couple of years back when the first draft was published. Note the date on the second link.
Intelligence fading....
Its probably because you just lost around 110,000 genes. It could happen to anyone.
Tequila: It's not just for breakfast anymore!
Science: Genome Surprize
Scientists still haven't found the gene for bad spelling...
sig
I need to know how many genes we have in Libraries of Congress - these numbers just don't make any sense otherwise.
sic transit gloria mundi
It does mean that we have great low level instruction optimization, however. Built-in compression, at the hardware level.
27k base pairs you say? Each one being one of a possible four, making it representable with two bits? Faboo... You can store a complete human blueprint in under 14KB. Lets start encoding and launching our codes all over creation, as self-extracting executables, of course. Homo Sapiens cum Code Red. Digital panspermia.
The REAL jabber has the user id: 13196
What you do today will cost you a day of your life
Damn you scientists.
That's nothing new, though - scientists have known a long time there's no scientific basis for the concept of "race" as applied to humans. It's a cultural construct.
Not to argue with your basic idea there, but how does culture determine the similarities then? The fact that most native Africans have dark skin, most Northern Europeans are relatively fair skinned, and most Asians are notably shorter than Native Americans? There has to be some genes doing something. Or some other mechanism we have yet to discover.
Our perception of 'race' is surely more exaggerated than the actual genetic differences alone justify, but race is more than genes. For instance: dictionary.com defines race as:
* A local geographic or global human population distinguished as a more or less distinct group by genetically transmitted physical characteristics.
* A group of people united or classified together on the basis of common history, nationality, or geographic distribution: the German race.
* A genealogical line; a lineage.
* Humans considered as a group.
So race is neither purely genetic, nor purely cultural. We forget that sometimes.
Tequila: It's not just for breakfast anymore!
Begun formally in 1990, the U.S. Human Genome Project is a 13-year effort coordinated by the U.S. Department of Energy and the National Institutes of Health. The project originally was planned to last 15 years, but rapid technological advances have accelerated the expected completion date to 2003. Project goals are to
- identify all the approximate 30,000 genes in human DNA,
- determine the sequences of the 3 billion chemical base pairs
that make up human DNA,
- store this information in databases,
- improve tools for data analysis,
- transfer related technologies to the private sector, and
- address the ethical, legal, and social issues (ELSI) that may
arise from the project.
To help achieve these goals, researchers also are studying the genetic makeup of several nonhuman organisms. These include the common human gut bacterium Escherichia coli, the fruit fly, and the laboratory mouse.A unique aspect of the U.S. Human Genome Project is that it is the first large scientific undertaking to address the ELSI implications that may arise from the project.
Another important feature of the project is the federal government's long-standing dedication to the transfer of technology to the private sector. By licensing technologies to private companies and awarding grants for innovative research, the project is catalyzing the multibillion-dollar U.S. biotechnology industry and fostering the development of new medical applications.
Sequence and Analysis of the human genome working draft was published in February, 2001, in Nature and Science. See an index of these papers and learn more about the insights gained from them.
For more background information on the U.S. Human Genome Project, see the following
What's a genome? And why is it important?
To understand more read
I hate liberals. If you are a liberal, do not reply.
scientist 1: Hey have you seen gene #40,001?
...In other news scientists revealed today that
we have substantially fewer genes than expected; between 27,000 and 40,000 as compared to an original estimate of 140,000. Experts say that this discovery means that chimpanzees are even more like humans than people are...
scientist 2: It was just here with the others next to my sandwich...Oh.
scientist 1: Great, you ate 40,001 through 140,000! Forget this.
scientist 2: But what'll I tell the press???
***
"What we've got now is what we'll have for all eternity"
Perhaps in the future we'll get to see this next to:
"Everything that can be invented has been invented." -Charles H. Duell
"640k should be enough for anybody." - Bill Gates
I grant that this particular case may seem less "philosophical" than the cases in the quotations above but a "stick a fork in it...it's done" mindset is not only arrogant but detrimental to science as well.
That may be, but race is still interesting.
Race is not much more than a way of classifying people based on appearance. It might also hint at a shared cultural background, but not always. But it is still potentially useful.
Nobody would say that the colour of a car should have anything to do with its handling. It's just paint, and has nothing to do with the insides. On the other hand, there are far more red sportscars than there are powder-blue ones.
If people are willing to accept that, maybe they'd be willing to look at other factors that happen to coincide with light skin tones or different-looking eyes. Unfortunately, any researcher wanting to look at this might as well put on a hood and join the KKK because people are so overly sensitive when it comes to race. If the environments different races evolved in were different enough to cause the obvious physical differences, wouldn't it be surprising if the differences stopped there? Even if the differences within a race are far greater than the differences between races, it would be interesting to see if there are tendencies towards something based on race.
He'll sue citing the DMCA.
The complexity of organisms is not solely determined by how many genes they have. There are many other factors. One of them is the expression level of different genes. Differentially expressed genes in different cells leads to different cell types, which form tissues, organs, and overall complicated organisms. There are also other ways of conveying information from one generation to the next other than genes. There is an entire epigenome out there -- non-bp modifications to the DNA (e.g., methylation of DNA) and DNA structure (e.g., methylation of Histone-3's at the Lys 4 and 9, v. acetylation at those sites, v. phosphorylation). This relates to imprinting. For interesting reading, do NCBI searches on the following expressions:
Epigenetics
Imprinting
Histone Code
Imprinting Histone Code
Various epigenetic (that is, above the DNA-bp level) states are epigenetically inherited. They often determine chromatin structure, and are involved in a war between maternal and paternal genomes, genetic conflict. And, they contribute to creating a much more cmplicated organism than the number of genes alone would indicate.
Also, it is important to notice that more complex eukaryotes tend to have more transcription factors, zinc-finger proteins, and so on and so forth. The number of regulatory proteins has mushroomed as organisms become more complicated. It is clear that one of the most important things in determining the complexity of organisms is the differential regulation of various genes.
social sciences can never use experience to verify their statemen
Not to undermine the significance at mapping the genes, but they're the first step. The next is proteins, the building blocks of life described in DNA. They do everything, so naturaly they are being studied closely by biologists and drug companies.
So what if there is fewer genes than expected? It means that the means of describing protiens is not linear. Protiens can fold four different ways, offering many different structural combinations.
The highest level biological system we understand completely is a species of yeast. For a human, the interactions that make the system work are almost unimagineably complex, because there are so many variables. We're just beginning to model them accurately.
Complexity of life is more than just genes.
While I'm certainly not a learned expert, as a new graduate of an Honours Genetics program in Canada, I feel I must point out a few misconceptions found in the story intro.
I let out an audible groan over the 'revelation' that the human genome contains at most 40,000 genes, compared to the original estimate of ~150,000. I was relieved when I noticed that the article linked to dated to 2001. This makes sense, since that discrepancy was first discussed during my courses over two years ago.
The other grain of salt that needs to taken is the idea of a "completed" genome. The human genome is nearly sequenced, however it the annotation of the genome that matters most. To place this into context, the genome of the fruit fly, Drosophila melanogaster, is over 75% annotated. Currently only a small portion of the human genome is annotated, that is to say, the roads are mapped, and the streets (or in this case, genes) are identified and their function characterized. This is one of the most essential tasks still facing biologists today. Without knowing all the potential genes, as well as their function and expression patterns, the human genome is no better a guide than using a globe to navigate the streets of Toronto (or New York, take your pick).
As it has been mentioned before, I won't delve too far into the fact that a given stretch of DNA can code for genes in two different directions, and in three different "frames" per direction. On top of this, the mRNA produced from the DNA can be spliced in numerous ways. A single expanse of DNA can produce countless different proteins - and its proteins, not genes, that carry out all the functions our body needs to survive.
Humans are extremely complex, but as we go about our 'very' important lives, it's humbling to know that on the surface, we do not contain many more genes than some other 'lesser' forms of life on this planet.
"Nokia is not a country, it's the capital of Finland!" -Moderated "Informative". Yeesh.
As far as I know, there is no easy method to distinguish a gene from other parts of DNA sequence. In order to get such an estimate heurictic algorithms that look for characteristic patterns in the sequence are used. Therefore it is hard to say about proofs. These are only estimates, which can be more or less justified. Searching methods are of course tested on other organisms which are better known (e.g. Drosophilia), but we are not really aware of differences and similarities in gene expression of mentioned fruit fly and human.
Besides the number of genes doesn't have to determine anything. It is just the number of different proteins that can be produced in the living cell. What makes an organism really complex is how and when these proteins are produced and this is determined by gene expression which is poorly understood. It can be compared to different methods of encoding. 8 bits are 8 different signals but offer 256 different combinations. If "complexity" of a living organism is exponential to the number of genes, than one gene makes a difference.
Dark-skinned is not a race. "Black" is a race -- and very few black people have actual black skin (much less black teeth!). Races are cultural constructs that may include genetic/physical characteristics in their definitions. Some physical characteristics are often considered (e.g. skin color) and some (earlobe attatchment, blood type) are generally ignored. Furthermore:
What's probably most significant, though, is that the races which do correspond to genetic traits make no sense as biological characterizations. They don't match actual genetic difference groups at all. This is what is meant by the statement that races are purely cultural.
Sig:Why copyright isn't a fundamental human right
Mobo finds you puny earthling, with your 40,000 genes, quite humorous, and worthy of being devoured.
The Kruger Dunning explains most post on
The assumption that each gene codes for one protein is usually false. But, regardless of that, there exists an additional "degree of freedom" that biological organisms can utilize in order to allow themselves to assume as many "states" of gene expression as possible.
The topic of stochastic gene expression is becoming more interesting recently because of further advances in studying single-cell gene expression and the design of genetic regulatory networks.
Because the concentrations of many gene regulatory proteins are so dilute/low, there exists significant fluctuations in the number of molecules that actually regulate the gene's expression. These fluctuations vary from time to time and from cell to cell, producing non-deterministic levels of gene expression. The non-determinism (called stochasticity) can cause some very interesting behavior that leads to numerous potential 'states' of gene expression versus a single, deterministic state.
So, on a very real basis, probability has a lot to do with how certain genes are expressed. Successful biological systems, however, hate random chance unless it's advantageous. These certain genes that utilize the internal noise of a "small" biological system do so because it gives some sort of advantage to them..either coding for numerous possible states with the least number of genes or for allowing the cell to randomly pick between possible states in order to create a heterogeneous cell population.
If you're interested in some scientific articles, try Adam Arkin's paper from 1998, detailing a stochastic simulation of a virus that attacks E. coli cells. The virus randomly selects whether it will replicate itself quickly and burst the cell open or integrate itself into the bacteria's genome and sit dormant. The probability of each event depends on the state of the bacteria at the time of infection. If the bacteria is starved, the virus goes dormant. If it's healthy, the virus goes into replication mode.
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Bam!!
remember, folks.. just because we have a genetic sequence is about 10% of the story. Proteomics is the next big thing, and there are a lot more protiens than genes.
filter: +3. Hey, look! all the trolls went away!
All of these observations of having 140,000 genes were made well before ANYTHING had been sequenced, worms, corn, or humans. That was way back in the ancient days of Genetics when geneticists didn't realize how much interaction and recombination there was between genes. Many of the gene estimates came from crude estimates involving antibodies in the early 80s. We knew that we had tens of thousands of antibodies and so they assumed we had oodles of genes to make antibodies. Geneticists realized later that antibodies are coded out about 1/100 as many genes which are have lower than average "quality control standards" than other genes. Antibodies are created from mixing and matching segments of genes.
The more research is published, this phenomenon becomes more and more frequent. So the Central Dogma of Genetics (DNA->RNA->Protien) is slowly breaking down. Genes don't code for just one protein.
"One touch of Darwin makes the whole world kin." George Bernard Shaw
It's been a popular misconception in the popular media for a long time that traits that are learned are malleable, whereas traits that are innate or genetic are not. This is not the case. The malleability of a trait depends on how it is implemented in the body, not on whether it is inborn or learned.
The simplistic view of the importance of genetic contribution probably stems from the way genetics is taught in school. Your eye color is genetically determined and eye color does not change. However, the reason why eye color does not change is not that it is inherited by genetic inheritance, but because eyes are constructed the way they are.
This is one of the reasons why psychologists worry much less about heritability of traits than they used to. The malleability of any given trait remains an empirical question. Your genes don't know how heritable they are.
For an interesting discussion of heritability and malleability, read Plomin et al's Behavioural Genetics - or the brief version here.
-- Rolf Lindgren, cand.psychol
But so what? What's this mean? All the news programs tell me how this is going to bring an end to disease a longer life for all of us etc., etc. But nobody ever tells how. And everybody is supposed to have unique DNA, so whose DNA have they decoded? Not mine. So how does this help me?
It seems to me there is an awful lot of hype surrounding the Human Genome Project.
I can print my kernel on A4 as 1's and 0's - Does this mean an end to security vunerablilities an better use of memory?
Do you mind, your karma has just run over my dogma.
Race is not much more than a way of classifying people based on appearance. It might also hint at a shared cultural background, but not always. But it is still potentially useful.
Well, for sociology nerds, it's important to remember that 'race' as a concept doesn't really exist outside of a discourse of oppressive relationships, since its historical origins as a concept were so bound up in the overdetermining of slavery as a 'natural' practice.Not that anyone who uses the term is being oppressive. You are right to some degree, that the term is often used as a way of pointing at appearance linked to geographic heritage. But that nasty history is carried along with the word and the way the institutions of the world deal with it. Yes, words like that always have complex meanings.
Anyone who examines the quagmire that is Race Politics in N.A. (which influences the discourse of race throughout the world) has to admit that oppression, repression, taboo, and resistance are not yet dissociated from the concept of race.
As the poet said, "race is a myth, but racism isn't."
Damn those pesky terrorists
Actually, the human genome is a huge hack. Half of it is commented-out code, a quarter is just there to get the preprocessor to work and emacs to highlight it legibly, and a quarter is actually just run through the preprocessor to make config files. Oh, and while the main package contains the compiler, the power supply is a separate package, with its own compiler which is basically the same. It's a wonder it manages to contain any genes at all.