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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."
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.
How about two American Indians a black baby?
So if that's not genetically-determined, nothing is.
If the article is trying to say we can't determine the race of a person from that person's DNA, then it's only correct because we can't read the genome - yet.
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.
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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.
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
No, a gene is not a base pair, it is a string of base pairs. I don't know how many, on average, but the relevant parts of our DNA (some 3 billion base pairs) occupy considerably more than 15K.
What was your point? That you're pontificating without even high-school knowledge on the subject?
Well I suppose that's par for the course on slashdot.
Actually no, still wrong. A genome is the entire complement of genes an organism possess, a chromosome is a relatively arbitrary unit in which the genome is broken into. I doubt any scientist ever suggested that "more chromosomes=more complex" seeing as how most higher plants have significantly more chromosomes than any animals. A gene on the other hand is a functional unit, it can code for one or more proteins but they have a well known beginning and end (both to us and to the transcription machinery). These three words are about as non-exchangable as three words can be. You noted you weren't "intending to be scientific", however you were commenting on a somewhat scientific article in a moderately well-read community. If you don't want anyone to insult you, don't comment on things you don't understand.
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.
While it seems that your facts are in order (cite provided below), your tact needs work.
By BILL GATES
c.1996 Bloomberg Business News
QUESTION: I read in a newspaper that in 1981 you said, ``640K of memory should be enough for anybody.'' What did you mean when you said this?
ANSWER: I've said some stupid things and some wrong things, but not that. No one involved in computers would ever say that a certain amount of memory is enough for all time.
I don't see why they should. More genes == more superiority? Who made up that rule?
The brightest minds of biology did, over 10 years ago... and so the central dogma of biology ("one gene => one protein => one function") was taught to a generation of students.
Of course, this completely misses two of the biggest results in the last few years: the acknowledgment of alternative splicing as a common phenomenon (10 years ago, people thought it happened in 5% of human genes, now we know it's more like 50%) and the identification of miRNAs as regulators of gene function.
But it's so hard to argue with dogma...
To within half a percent, pi seconds is a nanocentury. -- Tom Duff
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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You're right, it's a hell of a lot more than 15 K, but it's still pretty transportable.
"The question of whether a computer can think is no more interesting than that of whether a submarine can swim" -EWD
Yeah, but as I understand it, the vast majority of those 3 billion are just filler and don't belong to any gene, so it's even smaller than what would fit on a CD, I'd guess.
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
Rest of the quote is that he, the director of the patent office, was requesting more funding, and that
"Anyone that would deny my must think that everything that can be invented has been invented"
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The modern concept of race is that groups of people that are readily identifiable via a few physical traits (primarily skin color, but also face and eye shape, height, etc.) are more closely genetically related, on average, to each other than to they are to other groups.
This has been proven to be false.
It doesn't have to be false. Populations do diverge genetically, that's certain. And human populations could have diverged in ways that are expressed uniquely as gross anatomical differences. But they haven't.
A key word in that previous paragraph is "uniquely". You see, for something like skin color to be a reliable indicator of genetic relatedness, the skin color has to have a one-to-one correspondence with the genetic variation that causes it.[1] For example, I happen to have a rare genetic disease that is a mutation on the gene that controls collagen. As far as anyone knows, this mutation exists only among a few people in the world that have a common ancestor. So if you find this mutation, then you've found someone related to me. Put another way, if you find someone with the disease I have, they're related to me.
In contrast, there are other mutations on the collagen gene that exist among many unrelated people. It's a common mutation. If you find someone with that corresponding disease, there's no guarantee that they're related to someone else with that disease.
Now, the problem is that all of the features that are associated with how people define "race" are like the latter example, not the former. That is, genetically unrelated people can have dark skin. Dark skin can and has arisen among unrelated populations. Worse, dark and light skin has arisen among relatively closely related populations such that a given light skinned population is more closely related to a given dark skinned population than it is to another light skinned population. So, looking at the human race as a whole, skin color is an unreliable indicator of genetic relatedness.
Within a population that is reasonably restricted, however, it can be a reliable indicator of relatedness. Almost all African Americans have a common ancestor from west Africa. But west Africans are not closely related to some other dark skinned Africans. So, for example, while African Americans share a tendency to having the gene that causes sickle cell anemia, other dark skinned people--including many other African peoples--do not.
The reason this is all very important is because the modern idea of race has been assumed to have been validated on the basis of genetics. Furthermore, since it's assumed that members of a "race" are closely related genetically, and since it's obviously true that genetically closely related individuals are likely to share a lot of traits, it's been assumed that members of a race share lots of similar traits. Thus, people have argued about gross differences between races in the matter of intelligence, athletic ability, temperment, what have you. And if race did reliably indicate genetic relatedness, then these assumptions might have some merit. But since race is not an indicator of genetic relatedness, it can't be (in this respect[2]) an indicator of similarity in these traits.
Since the whole modern notion of race rests upon this assumption of relatedness and shared traits, and that notion is false, this is why some people say that the concept of race is scientifically false. They're not saying that genetics is false, or that genes don't control the expression of the various features associated with race. They are saying that the particular kind of relationship imagined between genetics and race doesn't exist.
And, in the end, what you're left with is a very messy sociological conception of race which has everything to do with local cultural standards and nothing at all to do with genetics in a meaningful way.
It also occurs to me that if one was drowning, yelling "Help! I'm drowning and I lost my bikini top" would probably be m