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."

Comments

Genome Surprize

[InterruptDescriptorT]

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.

I thought so.

[Capt'n Hector]

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.

Re:I thought so.

[Spy Hunter]

Yeah, I was astonished at the stupid claims being made in the article based on this percieved lack of genes.

The small number of genes is significant [because it means] we're not hard-wired

It means no such thing! It could just mean that fewer genes are necessary to hard-wire us. Nobody really knows how much effect particular genes have on us, so saying that 140,000 would be enough but 40,000 isn't enough is just spewing hot air.

The low number of genes means humans have as few as 300 more genes than a mouse and only twice the genes of the fruit fly. "A lot of people will find that philosophically disturbing," says theoretical biologist Jean-Michel Claverie

I don't see why they should. More genes == more superiority? Who made up that rule? How about "better genes == more superiority"?

The low number of genes [means] that there is no genetic basis for race.

Totally not true. Of course race has a genetic basis. It is inherited, after all. Black people have black children. It just means that the number of genes necessary to determine race is smaller than we thought.

...how have we become so much more complex than other creatures, whilst having relatively few extra genes.

I don't think it's any mystery. We're NOT "so much more complex!" The only part of us that is more complex is our brains. And animals have brains too, some of which are quite sophisticated by any measure of complexity.

Looks like people are having a field day speculating about what this low number could mean. I think it just means that we were wrong before, and we still don't have a clue about how big an effect single genes can really have on an organism.

Re:I thought so.

[JDevers]

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.

Re:I thought so.

[evilquaker]

The low number of genes means humans have as few as 300 more genes than a mouse and only twice the genes of the fruit fly. "A lot of people will find that philosophically disturbing," says theoretical biologist Jean-Michel Claverie

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...

Re:I thought so.

[skywire]

Of course race has a genetic basis. It is inherited, after all. Black people have black children.

If you were talking about skin colour, then this would make sense. But you are speaking about 'race', which is a word that is used to refer to a fuzzy concept that has no clear scientific definition. You might as well have said "Of course phlogiston flows. Things do change temperature, after all."

Re:I thought so.

[gilroy]

Blockquoth the poster:

I don't see why they should. More genes == more superiority? Who made up that rule? How about "better genes == more superiority"?

What the heck does "better genes" mean? For that matter, what does "more superiority"? Despite what everyone seems to want, evolution is not a moralistic process! There is no "superior" or "inferior". At best, there is "more fit" and "less fit" -- and even that is strongly location-dependent and time-evolving. In terms of survival fitness, it can be argued that, say, bacteria -- or insects -- way outperform humans. Sure, they don't build cathedrals or rocket ships, but what the heck does evolution care?

Re:I thought so.

[Rutulian]

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.

Actually that is not the central dogma of biology. The central dogma is DNA -> RNA -> Polypeptide (Ref: Russell, Genetics, 1998). The one-gene one-enzyme hypothesis was proposed a long time ago, and yes it did earn a Nobel Prize, but it has since been altered to the one-gene one-polypeptide hypothesis. Gene expression has proved to be much more complicated than anyone initially thought.

Re:I thought so.

[gene_tailor]

>Just because an idea is imprecise does not mean it does not exist

It may exist in sociology, but not in genetics. Race is not a genetically valid concept. It is true that there are genetic differences between groups, but genetic studies have found that the amount of variation WITHIN each group is larger than that AMONG various groups. Attempts to predict race/ethnicity etc. from genetic sequence have all failed. The few differences among our genes that produce physically visible traits are tiny compared to the number of possible variations visible at the molecular level.

Re:I thought so.

[kmellis]

People are trying to explain this in different ways, but let's make it clear and simple:

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.

Beware

[Anonymous Coward]

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.

Implications

[Pettifogger]

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.

Not a new observation

[zach_smith]

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.

Re:This is Great

[Pharmboy]

Intelligence fading....

Its probably because you just lost around 110,000 genes. It could happen to anyone.

Apparentlysss

[ekephart]

Science: Genome Surprize
Scientists still haven't found the gene for bad spelling...

Article's numbers not clear

[glwtta]

I need to know how many genes we have in Libraries of Congress - these numbers just don't make any sense otherwise.

This does not mean we're simple

[jabber01]

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.

Re:This does not mean we're simple

[vondo]

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.

Re:This does not mean we're simple

[Galvatron]

Assuming 3 billion base pairs, that'd be 1.5 billion bytes, or just under 1.4 gigabytes. Since there are a small number of 3 base pair groupings that make up all of the amino acids (if I remember my high school biology, which I may not, feel free to correct me), this is probably heavily compressible. We should be able to wedge it onto a CD-ROM. Even uncompressed, your genome will fit on a DVD.

You're right, it's a hell of a lot more than 15 K, but it's still pretty transportable.

Suddenly

[cyril3]

I'm only half the man I used to be.

Damn you scientists.

Re:Just for comparison's sake...

[Pharmboy]

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.

Background Info

[Acidic_Diarrhea]

Want To Know What The Human Genome Project Is?

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

• HGP Goals (1998-2003)
• HGP Progress
• HGP History
• Human Genome News

What's a genome? And why is it important?

• A genome is all the DNA in an organism, including its genes. Genes carry information for making all the proteins required by all organisms. These proteins determine, among other things, how the organism looks, how well its body metabolizes food or fights infection, and sometimes even how it behaves.
• DNA is made up of four similar chemicals (called bases and abbreviated A, T, C, and G) that are repeated millions or billions of times throughout a genome. The human genome, for example, has 3 billion pairs of bases.
• The particular order of As, Ts, Cs, and Gs is extremely important. The order underlies all of life's diversity, even dictating whether an organism is human or another species such as yeast, rice, or fruit fly, all of which have their own genomes and are themselves the focus of genome projects. Because all organisms are related through similarities in DNA sequences, insights gained from nonhuman genomes often lead to new knowledge about human biology.

  To understand more read

  • The Science Behind the Human Genome Project: Understanding the Basics

A day at the genome office

[boatboy]

scientist 1: Hey have you seen gene #40,001?
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???

***
...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...

The less one makes declarative statements...

[eidechse]

"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.

Don't tell God...

[gilesjuk]

He'll sue citing the DMCA.

The Real Human Genome Project

[Mars Ultor]

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.

Re:Just for comparison's sake...

[dspeyer]

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.

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:

• USA custom dictates that an individual with one great-great-grandfather from Nigeria and the rest from England is black, completely irrespective of any alleles the individual may actually express or carry.
• USA custom acknowledges "Hispanic" as a race, even though it carries no genetic correlation. It is roughly defined as an individual who's native language is an American dialect of Spanish, or the decendant of such a person to the fourth generation. Except Jamacans, who might be black. And including Haitians and Brazilians, or something like that.
• Mexican custom dictates that an individual with one nigerian parent and one Castillian is black, mulatto, or white depending on the individual's net income. (Disclaimer: I haven't been to Mexico -- this is the finding of some random ethnographer.)

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.

On the Topic of Determinism vs. Stochasticity...

[Salis]

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.

Salis

genomics is only the first step

[EngMedic]

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.

"genetic" does not mean "hard-wired"

[roffe]

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.