Scientists Analyze Chromosomes 2 and 4: Discover Largest "Gene Deserts"

National Human Genome Research Institute ^ | 06 April 2005 | Staff

[PatrickHenry]

A detailed analysis of chromosomes 2 and 4 has detected the largest "gene deserts" known in the human genome and uncovered more evidence that human chromosome 2 arose from the fusion of two ancestral ape chromosomes, researchers supported by the National Human Genome Research Institute (NHGRI), part of the National Institutes of Health (NIH), reported today.

In a study published in the April 7 issue of the journal Nature, a multi-institution team, led by [load of names deleted, but available in the original article].

"This analysis is an impressive achievement that will deepen our understanding of the human genome and speed the discovery of genes related to human health and disease. In addition, these findings provide exciting new insights into the structure and evolution of mammalian genomes," said Francis S. Collins, M.D., Ph.D., director of NHGRI, which led the U.S. component of the Human Genome Project along with the DOE.

Chromosome 4 has long been of interest to the medical community because it holds the gene for Huntington's disease, polycystic kidney disease, a form of muscular dystrophy and a variety of other inherited disorders. Chromosome 2 is noteworthy for being the second largest human chromosome, trailing only chromosome 1 in size. It is also home to the gene with the longest known, protein-coding sequence - a 280,000 base pair gene that codes for a muscle protein, called titin, which is 33,000 amino acids long.

One of the central goals of the effort to analyze the human genome is the identification of all genes, which are generally defined as stretches of DNA that code for particular proteins. The new analysis confirmed the existence of 1,346 protein-coding genes on chromosome 2 and 796 protein-coding genes on chromosome 4.

As part of their examination of chromosome 4, the researchers found what are believed to be the largest "gene deserts" yet discovered in the human genome sequence. These regions of the genome are called gene deserts because they are devoid of any protein-coding genes. However, researchers suspect such regions are important to human biology because they have been conserved throughout the evolution of mammals and birds, and work is now underway to figure out their exact functions.

Humans have 23 pairs of chromosomes - one less pair than chimpanzees, gorillas, orangutans and other great apes. For more than two decades, researchers have thought human chromosome 2 was produced as the result of the fusion of two mid-sized ape chromosomes and a Seattle group located the fusion site in 2002.

In the latest analysis, researchers searched the chromosome's DNA sequence for the relics of the center (centromere) of the ape chromosome that was inactivated upon fusion with the other ape chromosome. They subsequently identified a 36,000 base pair stretch of DNA sequence that likely marks the precise location of the inactived centromere. That tract is characterized by a type of DNA duplication, known as alpha satellite repeats, that is a hallmark of centromeres. In addition, the tract is flanked by an unusual abundance of another type of DNA duplication, called a segmental duplication.

"These data raise the possibility of a new tool for studying genome evolution. We may be able to find other chromosomes that have disappeared over the course of time by searching other mammals' DNA for similar patterns of duplication," said Richard K. Wilson, Ph.D., director of the Washington University School of Medicine's Genome Sequencing Center and senior author of the study.

In another intriguing finding, the researchers identified a messenger RNA (mRNA) transcript from a gene on chromosome 2 that possibly may produce a protein unique to humans and chimps. Scientists have tentative evidence that the gene may be used to make a protein in the brain and the testes. The team also identified "hypervariable" regions in which genes contain variations that may lead to the production of altered proteins unique to humans. The functions of the altered proteins are not known, and researchers emphasized that their findings still require "cautious evaluation."

In October 2004, the International Human Genome Sequencing Consortium published its scientific description of the finished human genome sequence in Nature. Detailed annotations and analyses have already been published for chromosomes 5, 6, 7, 9, 10, 13, 14, 16, 19, 20, 21, 22, X and Y. Publications describing the remaining chromosomes are forthcoming.

The sequence of chromosomes 2 and 4, as well as the rest of the human genome sequence, can be accessed through the following public databases: GenBank (www.ncbi.nih.gov/Genbank) at NIH's National Center for Biotechnology Information (NCBI); the UCSC Genome Browser (www.genome.ucsc.edu) at the University of California at Santa Cruz; the Ensembl Genome Browser (www.ensembl.org) at the Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute; the DNA Data Bank of Japan (www.ddbj.nig.ac.jp); and EMBL-Bank (www.ebi.ac.uk/embl/index.html) at EMBL's Nucleotide Sequence Database. [Links in original article.]

NHGRI is one of the 27 institutes and centers at NIH, an agency of the Department of Health and Human Services. The NHGRI Division of Extramural Research supports grants for research and for training and career development at sites nationwide. Additional information about NHGRI can be found at www.genome.gov.

[Ahban]

Yes. I accept God for who the Bible says He is, and love Him for it. He is not only infinitely merciful, but infinitley just. I agree with the U.S. Supreme court that capital punishment for certain juveniles is necessary (though He also reveals in Ezekiel 33 that He does not delight in the death of the wicked, but rather that they turn from thier ways and repent.. In the part of the law you name, it is not clear to me that the "children" to be stoned to death are not in their 20s anyway.

Is that any less just than our current system that takes childern from parents just for spanking them in public? That does not allow the parents to discipline an unruly child so they grow up wild and police have to shoot them later?

The "slaves" were not the sort of slaves that Americans once kidnapped from Africa. A better translation would be "bond servatns". After 7 years they were supposed to be let go, unless they decided they wanted to stay with their master for life. There are a lot of people out there today who are too plain stupid to successfully navigate the modern world on their own. They would be better off if they attached themselves to some well to do person and became their household bond servant.

The reason this God does not seem cruel or harsh is 1) I am not brainwashed by liberal propaganda and 2) Jesus took the penalty for sin that I deserved. God is not strict on us but lax on Himself.

[exDemMom]

This is a tired argument and your "theory" is just that. Wild speculation and innuendo, assuming this that the other thing draw conclusions only to what you want to believe.

So, I take it you also doubt the theory of electromagnetism? The theory of gravity?

May I suggest that you find out what the word "theory" means, in the scientific sense. Evolution (and gravitation and electromagnetism) are theories because they are the best descriptions that explain the known facts and predict new ones. Scientists are not given to "wild speculation and innuendo"; if you want that kind of stuff, you need to go to DU or some conspiracy website or something. We scientists, we're driven to find out how the world works. When we speculate, we set up experiments to prove or disprove our speculation. And we are ruthless about trying to debunk ourselves.

[Echo Talon]

If these "scientists" weren't so hellbent on trying to prove this theory maybe they could devote their time, energy and resource's to something useful like curing diseases like cancer and diabetes I think that would be a much more noble task.

[Echo Talon]

electromagnetism? The theory of gravity?

Those can be proven and replicated in a lab. Man evolving from a single cell organism however is speculation and could never be replicated nor proven.

[exDemMom]

If these "scientists" weren't so hellbent on trying to prove this theory maybe they could devote their time, energy and resource's to something useful like curing diseases like cancer and diabetes I think that would be a much more noble task.

Um, what is it, exactly, that you think we do? That we're spending BILLIONS of YOUR tax money doing? There are a few people working specifically on refining--not proving, but refining, the theory of evolution, but most of us are just using the theory to understand exactly what is going on at the molecular level. If we didn't have the unifying theory of evolution as a basis, most of the rest of our work--like curing cancer and diabetes--wouldn't be possible. It would be like trying to develop a new television technology while ignoring the theory of electromagnetism.

[Echo Talon]

oh bs.

[exDemMom]

Those can be proven and replicated in a lab. Man evolving from a single cell organism however is speculation and could never be replicated nor proven.

Really? How do you replicate gravity in a lab? How do you "prove" electricity? Have you ever studied physics? (Or any science, for that matter?) No one really understands gravity or electricity.

Apparently, you think that the word "theory" is a synonym of "supposition." It is not. In science, a theory is the unifying explanation for all of the known facts, and it can be used to predict other facts which are testable. You cannot do better than a theory in science.

All I can say is, I'm sorry you feel your faith is not strong enough to stand in the light of what we know about the world. God didn't disappear just because we discovered evolution.

[hemi dawg]

The very notion of "further evolutionary advancement" is not in alignment with God's design. The only metric which God applies to His species is survival. By that metric, we have a long way to go before approaching that of "superior" species such as cockroaches and snails.

The survival metric is not a straight line. Sometimes a specific feature is good for survival, sometimes it is not so good--a changing environment demands adaptabiliy to maximize survival. We are "evolutionarily advanced" only to the extent that we are adaptable to our changing environment.

[pepsionice]

I think the best analysis here...is that its like going into a grocery store and buying materials for a cake...there are always the same basic 3 ingredients...cake mix, eggs, and water...and then there are the "others" which you mix in as well for the different taste.

[Echo Talon]

I'm sorry just feel your trolling. I'm done with this thead, keep believing you nonsense and keep trying to come up with the answer of, where did the first spark of life come from? Who created it?

[sakic]

The "slaves" were not the sort of slaves that Americans once kidnapped from Africa. A better translation would be "bond servatns". After 7 years they were supposed to be let go, unless they decided they wanted to stay with their master for life. There are a lot of people out there today who are too plain stupid to successfully navigate the modern world on their own. They would be better off if they attached themselves to some well to do person and became their household bond servant.

So if your child was a "bond servant" it would be just fine. I notice that you failed to address that "God" said it was okay to beat your "bond servants". If your child was a bond servant it must be encouraging to your child that it would be okay with you for your kid to be beaten by his master.

[VadeRetro]

I wouldn't brag about it. Next you'll be tossing up pea soup over people.

[Ahban]

Do you beleive that schools should be allowed to give corporal punsihment?

What about caning of delinquint youths by the government such as is practiced in Hong Long?

[microgood]

In general, scientists are very aware of the limits of knowledge in their field. However, the media filter makes things sound very strange and there are people with a political agenda who will use anything to get their way.

It's good to know many scientists are.

In the case of organisms growing arms and legs, Ichneumon's post documents the fossil evidence of this occurring.

I have seen many of his postings but I am looking for creatures with partially formed arms or legs that have no apparent purpose and all I ever saw him come up with is that one bird with a claw that becomes a wing or something. A lot of his posts are other theories supporting this theory. But I will keep on looking.

The problem for anti-science is that there is an enormous amount of fossil evidence.

It's not the evidence I have a problem with although dating things is based on a large set of assumptions as well, it is in the interpretation, and the common characteristic = common ancestry is something I find troubling even though the dating of the fossils seems to bolster it.

So they've chosen to pick on something well documented, like the development of flagella or eyes (there are over 3500 different kinds), but have ignored truly complex structures like the brain.

I agree with you on this. It is easier to argue that a leg or an arm or brain is irreducibly complex than it is a flagella, and the refutation made by Miller(as weak as it was) that part of the flagella could exist as a smaller component with a different purpose, is not so easy to do with an arm, which would require probably millions of years to develop, and would not really have any other purpose except some sort of aberration for most of that time until it became a fully functioning arm(you think we would see fossil evidence of partial arms,etc. but would even see that stuff now, but all species seem completely formed).

Evolutionary biology is still the best explanation.

It may be the best one currently, but may not be correct. It is very difficult to piece together what happenened millions of years ago with an incomplete view of the past. Even when a plane crashes today, we can barely find out what happened even with our black boxes and technology because we weren't there and noone survived to tell us.

If we're lucky, we'll be here long enough to see a pill that can grow someone a new kidney.

I hope so. Maybe someone with mutate a brain big enough to figure that out.

[Thatcherite]

Yes. I accept God for who the Bible says He is, and love Him for it. He is not only infinitely merciful, but infinitley just. I agree with the U.S. Supreme court that capital punishment for certain juveniles is necessary (though He also reveals in Ezekiel 33 that He does not delight in the death of the wicked, but rather that they turn from thier ways and repent.. In the part of the law you name, it is not clear to me that the "children" to be stoned to death are not in their 20s anyway.

Exodus 21:17 and Leviticus 20:9 specify putting to death those who curse their parents. Deuteronomy 21:18 specifies putting to death by stoning children who are "stubborn and rebellious". (No mention of serious crimes being required in either case). Do you obey God's law in this matter? If not then why not? Would you obey God's law and support your neighbour if he asked you to help him stone his children to death for being stubborn and rebellious as God requires? Would that be OK if the children were in their 20's?

The "slaves" were not the sort of slaves that Americans once kidnapped from Africa. A better translation would be "bond servatns". After 7 years they were supposed to be let go, unless they decided they wanted to stay with their master for life. There are a lot of people out there today who are too plain stupid to successfully navigate the modern world on their own. They would be better off if they attached themselves to some well to do person and became their household bond servant.

The Africans taken as slaves to the New World were not largely kidnapped; they were largely purchased in the markets implied and endorsed by implication in Leviticus 25:44-46. I take it that you see yourself as the "protector" of such a poor inadequate who ought to have the sense to decide to be a bond-servant. I think you need to read Exodus 21 1-10 a bit more carefully. Also Leviticus 25 44-46, and Exodus 21 20-21. Buying and selling slaves as permanent property? Sex slavery? Holding families hostage against a time-expired bond-servant "deciding" to become a slave? Beating slaves? (which was also endorsed by Jesus in the Bible). Would you do those things? Would you be happy with your neighbour obeying God and doing those things?

[stremba]

Evolution doesn't say. Evolution starts when life originates and proceeds from there. There is no scientific theory about the origin of life. There are several competing hypotheses about how life originated, but these have not yet risen to the level of theory. In short, the best scientific answer is "we don't know, but we're working on it."

[stremba]

Please state the theory of gravity and how it can be "proven" in the lab. HINT: you can't prove any theory in the lab. All you can do is subject a theory to further tests and gather more evidence in its favor.

[Ahban]

Before I answer first you answer my questions to sakic in #313.

[Thatcherite]

I have no problem with the corporal punishment of delinquent youths by schools or states as long as a judicial process is followed in determining the need for such punishment in which the youths have the opportunity to defend themselves. Such punishments should be proportionate to the crime. We aren't talking about that; we are talking about capital punishment for minor offences (instructed by the Bible) and slaveholding (endorsed by the Bible). Are you supporting these practices? If not why not?

[Ahban]

You do well to consider the scriptures, and look to them. When studied with faith, they bring life and peace.

Leviticus 25:44-46 was not an endorsement of slavery, but an effort to limit it. This is clear if you read the surrounding verses. The scriptures serve as tutor for mankind, bringing him from a state of barbarity to a state of enlightenment. The main point of the passage you cite, when surrounding verses are considered, is that you are not to treat your fellow Hebrew (your neighbor) like that. Jesus then showed us that our neighbor is anyone who is around us. Mankind is tutored by God at a rate we can handle it.


I will have to address your points on capital punishment tomorrow. This morning I wold like to address your points on corporal punishment.


The slaves that you say Americans bought fair and square were mostly kidnapped, and as such do not compare with a 'bond servant" agreement.

You seem to think it fine for the State/Schools to beat on children but not OK for a Master that the parent has chosen to do the same. Wild children have to be disciplined for their own good and the good of society. On that we agree. What choice does the parent have about their government? In these days of complusory attendence laws what choice do they have in schools (unless they homeschool). At least they can pick their master.

I see the Bible's solution as less statist and more free than the socialist position that the state should have a monopoly on force. The more power parents (and their chosen masters have) to use force to discipline then the less force the state will need (and the less power it need have).

Perhaps you live among civilized, secular people who do not need a caning to stay out of trouble. Good for them, but you should not assume that the whole world is like them.

As for "slavery" being unchristian, it is in a way. Philemon is a good study on that, he was a run away slave and Paul teaches the next lesson on how "slaves" ought to be treated. The Bible tutors humanity to the final step.

Frederick Douglass was a former slave, and a CHristian. He observed that while the Bible permitted men to be masters it did not permit them to be bad ones. If he can content himself with that and still have faith in God, despite living as a slave, then Thatcherite is surely without excuse in his efforts to condemn his Maker.