Naked Science Forum
Life Sciences => Cells, Microbes & Viruses => Topic started by: tweener on 31/03/2004 05:09:37
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I don't know too much about DNA, but I understand that while the molecule is huge, there are large sections that just repeat the same codes over and over, there are some sections that are genes but they are not expressed at all, and then there are the genes that are expressed and actually do something. Inefficient, but what do you expect from 4 billion years of trial and error for a design.
So, my question is how much of our DNA is actually functional genes and how much is just there. Do we really know the answer yet?
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John - The Eternal Pessimist.
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No we don't really know the answer yet. We've pretty much found all the genes now that we have the genome sequenced. It came out to be about 30,000 genes (much lower than most estimates). I don't have a percentage number for you off the top of my head as far as how much of the genome that is but its pretty small (I would guess like 2% but thats totally a guess).
Howvere that doesn't mean that thats all we use. For instance remember that how a gene is expressed depends largely on the structural conformation of the DNA/chromosome and how it is folded on itself. While I will admit even this does not account for anywhere near the amount of non gene DNA that we have, it doesn't mean that the rest is just there. The old term "junk DNA" has all been thrown out of the scientific vocabulary. Most scientists that i know of hypothisize that the rest of the DNA is used for something. Remember that just because we don't know somethings function doesn't mean that it doesn't have one.
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We were taught that some of the repeated nonsense (not a gene) strand is unique from person to person and can be used for DNA fingerprinting.
Tom
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Read Darwin's ... (something can't remember what) by Greg Bear, it's a fantastic novel about retroviruses, it's really exciting
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yes, nilmot, you are right those ARE the parts taht are used for DNA fingerprinting, but I don't think that evolution produced those for us so that we could convieniently catch criminals. there still ahs to be some biological function to them.
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I never assume that because we don't know the function of something means it has no function. And, I've never heard of "junk DNA". I was just curious.
I read "Darwin's Children" a little while back. It was ok, but I thought a little implausible and overdone. I haven't read any of the other "Darwin's ..." books yet, but I probably will sometime.
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John - The Eternal Pessimist.
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Up until not very long ago "junk DNA" was the common nomenclature, and most people paid little attenbtion to that DNA and just assumed that it served no function.
I hear so much about those "Darwin's..." books but know nothing about them. Could someone explain to me?
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well, all i know is that a small difference or strand could really change alot because i do know that we and monkeys have only one difference of strand at the base of things, so it makes a BIG difference, they are real important
darwin, actually he really doesn't believe in evolution he said that there is no possisble way we could have evolved at his death bed but he also did say survival of the fittest, the weak must die
Greetings in Christ Jesus my Lord
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actually in the repeat segments that tweener is referring to you can have HUGE changes in DNA sequence that often show no effect on pheno type. But in other regions, a single base pair change can cause a drastic change in phenotype.
Darwin DID believe in evolution, he's co-credited for characterizing the theory. Howvere you are right that before he died he said that he didn't believe that we could have came from such lower organisms that his theory predicted. This was just because at his time so little was known about science, that it was almost impossible to comprehend something as unorthodox as humans evolving from single celled organisms. So he did believe in evolution, just micro-scale evolutio, even though he came up with the theory that suggested macro-scale evolution.
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and he was hedging his bets on his death bed!
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I've read that there are scientists that are saying the theory of evolution and natural selection is wrong. That "evolution" occurs as simply random mutations and nothing more. A gene then becomes predominant (or not) in a species simply by the random propagation through the generations. I don't know about it, but it sounds interesting.
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John - The Eternal Pessimist.
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Evolution DOES come about due to random mutations in the genome of a single member of a species. There is a chance that this gene could beat the odds and work its way to predominance within the population without neccesarily being a more adventageous trait. Odds are strongly against this though.
Evolution is merely a game of odds. Saying that because a trait COULD work its way into a population without being adventageous means natural selection does not exist is like saying that just because you CAN win at roulette by betting on a single number, means you WILL every time (I'm not sure if that analogy made as much sense as I thought it would).
Remember that natural selection is NOT what causes evloution, or even what drives it, but simply what steers it in the dirrection that it goes. And its all an odds game.
While there are several mechanisms by which evolution comonly occurs, natural selection is an underlying factor in almost all of them. It can also be experimentally shown quite easily. If you want a good example of this do a google serch for "industrial melanism" possibly the best naturally designed experiment ever; it really shows natural selection at work.
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Justin
I'm not really sure where you get the idea that Darwin (the guy who first described evolution) "did not believe we could have come from such lower organisms" - he seems pretty certain on that fact in the closing conclusions of "The Origin of Species" :
"Analogy would lead me one step further, namely, to the belief that all animals and plants have descended from some one prototype...all living things have much in common, in their chemical composition, their germinal vesicles, their cellular structure, and their laws of growth and reproduction...the same poison often similarly affects plants and animals; or that the poison secreted by the gall-fly produces monstrous growths on the wild rose or oak-tree. Therefore I should infer from analogy that probably all the organic beings which have ever lived on this earth have descended from some one primordial form, into which life was first breathed..."
which you can read online here :
http://www.literature.org/authors/darwin-charles/the-origin-of-species/
Chris
"I never forget a face, but in your case I'll make an exception"
- Groucho Marx
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The protein coding DNA they have decoded is about 3%
of the total ammount of DNA of the top of my head. some
say the other DNA is junk, i really don't think so. what
does the other 97% do?
any suggestions from our intellectual hosts? :)
ebzZzZ
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Don't forget about mitochondrial DNA, too. Some genes are expressed in conjunction with or solely through mDNA.
It's a comparatively small amount to what's in the nucleus, but not insignificant compare the how much of the nuclear DNA we know to be "active"
Also, females (XX chromosomal ones anyway) lose an entire chromosome's gene expression. One of their X chromosomes supercoils and methlyates in each cell so that traits from only one X chromosome are expressed.
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Good to see you back on the forum Jay!
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John - The Eternal Pessimist.
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Just to chip in Jay (and yes it's nice to see you), that you are correct, when a cell contains more than one X chromosome the additional X chromosomes are shut off, on a random basis, by a process called Lyonisation (named after the British discoverer of the phenomenon (in 1961), Mary Lyon).
The shut off, or inactivated, chromosomes form a small dense aggregation in the nucleus called a Barr Body (after Barr and Bertram, 1949).
However, not all of the genes on the Lyonised X chromosomes are shut off. Some - like XIST (which initiates the inactivation), and ZFK ((which codes for a protein involved in the production of eggs and sperm) - remain active (by an as-yet undefined mechanism). You can see this clinically in patients with conditions like Kleinfelters Syndrome in which individuals have an extra X chromosome. Phenotypically these people are male, but looking at their cells you find they have XXY - 2 X chromosomes (like a woman) plus a Y chromosome (like a male). If the extra X were completely shut off these people would be normal, but in reality they are often infertile and may show below-average intelligence.
Chris
"I never forget a face, but in your case I'll make an exception"
- Groucho Marx
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Read Darwin's ... (something can't remember what) by Greg Bear, it's a fantastic novel about retroviruses, it's really exciting
Am I dead? Am I alive? I'm both!
(https://www.thenakedscientists.com/forum/proxy.php?request=http%3A%2F%2Fwww.stupid-boy.com%2Fsmilies%2Fkao%2Fotn%2Fcat.gif&hash=e4b91a72c020cc1c5d28487fff5428f1)
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yes, nilmot, you are right those ARE the parts taht are used for DNA fingerprinting, but I don't think that evolution produced those for us so that we could convieniently catch criminals. there still ahs to be some biological function to them.
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I never assume that because we don't know the function of something means it has no function. And, I've never heard of "junk DNA". I was just curious.
I read "Darwin's Children" a little while back. It was ok, but I thought a little implausible and overdone. I haven't read any of the other "Darwin's ..." books yet, but I probably will sometime.
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John - The Eternal Pessimist.
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Up until not very long ago "junk DNA" was the common nomenclature, and most people paid little attenbtion to that DNA and just assumed that it served no function.
I hear so much about those "Darwin's..." books but know nothing about them. Could someone explain to me?
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well, all i know is that a small difference or strand could really change alot because i do know that we and monkeys have only one difference of strand at the base of things, so it makes a BIG difference, they are real important
darwin, actually he really doesn't believe in evolution he said that there is no possisble way we could have evolved at his death bed but he also did say survival of the fittest, the weak must die
Greetings in Christ Jesus my Lord
-
actually in the repeat segments that tweener is referring to you can have HUGE changes in DNA sequence that often show no effect on pheno type. But in other regions, a single base pair change can cause a drastic change in phenotype.
Darwin DID believe in evolution, he's co-credited for characterizing the theory. Howvere you are right that before he died he said that he didn't believe that we could have came from such lower organisms that his theory predicted. This was just because at his time so little was known about science, that it was almost impossible to comprehend something as unorthodox as humans evolving from single celled organisms. So he did believe in evolution, just micro-scale evolutio, even though he came up with the theory that suggested macro-scale evolution.
This is a signature.... AND YOU WILL LIKE IT!!
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and he was hedging his bets on his death bed!
-
I've read that there are scientists that are saying the theory of evolution and natural selection is wrong. That "evolution" occurs as simply random mutations and nothing more. A gene then becomes predominant (or not) in a species simply by the random propagation through the generations. I don't know about it, but it sounds interesting.
----
John - The Eternal Pessimist.
-
Evolution DOES come about due to random mutations in the genome of a single member of a species. There is a chance that this gene could beat the odds and work its way to predominance within the population without neccesarily being a more adventageous trait. Odds are strongly against this though.
Evolution is merely a game of odds. Saying that because a trait COULD work its way into a population without being adventageous means natural selection does not exist is like saying that just because you CAN win at roulette by betting on a single number, means you WILL every time (I'm not sure if that analogy made as much sense as I thought it would).
Remember that natural selection is NOT what causes evloution, or even what drives it, but simply what steers it in the dirrection that it goes. And its all an odds game.
While there are several mechanisms by which evolution comonly occurs, natural selection is an underlying factor in almost all of them. It can also be experimentally shown quite easily. If you want a good example of this do a google serch for "industrial melanism" possibly the best naturally designed experiment ever; it really shows natural selection at work.
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-
Justin
I'm not really sure where you get the idea that Darwin (the guy who first described evolution) "did not believe we could have come from such lower organisms" - he seems pretty certain on that fact in the closing conclusions of "The Origin of Species" :
"Analogy would lead me one step further, namely, to the belief that all animals and plants have descended from some one prototype...all living things have much in common, in their chemical composition, their germinal vesicles, their cellular structure, and their laws of growth and reproduction...the same poison often similarly affects plants and animals; or that the poison secreted by the gall-fly produces monstrous growths on the wild rose or oak-tree. Therefore I should infer from analogy that probably all the organic beings which have ever lived on this earth have descended from some one primordial form, into which life was first breathed..."
which you can read online here :
http://www.literature.org/authors/darwin-charles/the-origin-of-species/
Chris
"I never forget a face, but in your case I'll make an exception"
- Groucho Marx
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The protein coding DNA they have decoded is about 3%
of the total ammount of DNA of the top of my head. some
say the other DNA is junk, i really don't think so. what
does the other 97% do?
any suggestions from our intellectual hosts? :)
ebzZzZ
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Don't forget about mitochondrial DNA, too. Some genes are expressed in conjunction with or solely through mDNA.
It's a comparatively small amount to what's in the nucleus, but not insignificant compare the how much of the nuclear DNA we know to be "active"
Also, females (XX chromosomal ones anyway) lose an entire chromosome's gene expression. One of their X chromosomes supercoils and methlyates in each cell so that traits from only one X chromosome are expressed.
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Good to see you back on the forum Jay!
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John - The Eternal Pessimist.
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Just to chip in Jay (and yes it's nice to see you), that you are correct, when a cell contains more than one X chromosome the additional X chromosomes are shut off, on a random basis, by a process called Lyonisation (named after the British discoverer of the phenomenon (in 1961), Mary Lyon).
The shut off, or inactivated, chromosomes form a small dense aggregation in the nucleus called a Barr Body (after Barr and Bertram, 1949).
However, not all of the genes on the Lyonised X chromosomes are shut off. Some - like XIST (which initiates the inactivation), and ZFK ((which codes for a protein involved in the production of eggs and sperm) - remain active (by an as-yet undefined mechanism). You can see this clinically in patients with conditions like Kleinfelters Syndrome in which individuals have an extra X chromosome. Phenotypically these people are male, but looking at their cells you find they have XXY - 2 X chromosomes (like a woman) plus a Y chromosome (like a male). If the extra X were completely shut off these people would be normal, but in reality they are often infertile and may show below-average intelligence.
Chris
"I never forget a face, but in your case I'll make an exception"
- Groucho Marx
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To get back to the subject of this thread, which was "how much of our DNA is actually used ?", a new article has jsut been published on the site by Jamil Bacha which gives an excellent overview of this subject and introduces the concept of DNA transposons - quite literally a form of biolgical SPAM ! Here's the link :
http://www.thenakedscientists.com/HTML/articles/article/jamilcolumn1.htm
Chris
"I never forget a face, but in your case I'll make an exception"
- Groucho Marx
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That's a neat article Chris!
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John - The Eternal Pessimist.
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Yes, I am back from a brief hiatus. School has been extraordinarily difficult this semester, I took on a research project, and I recently took the MCAT so my time has been stretched thin. =)
Chris, what is it about aneuploidal disorders like Kleinfelters that cause mental retardation, anyway? Is it too much of a protein being expressed that harms mental development as an infant or is it a mitotic dysfunction that screws with the fetus' development causing them to be born that way?
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Is Kleinfelters the one that can effect fetuses if the mother is exposed to cat litter/feces?
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No, that's toxoplasmosis, it's caused by an infectious protozoan Toxoplasma gondii.
Kleinfelter's is a genetic defect where a male has an extra X chromosome, presumably from an error during meiosis I. The sex chromosomes are supposed to separate along with the rest of the homologous pairs leaving only one sex chromosome in each gamete. (50/50 X and Y in males, only X in females) If for some reason the sex chomosomes pair does not separate, the gamete is left with 2 X or 2 Y chromosomes. Let's say a Y male gamete joins with an XX egg. The embryo then has an extra X chromosome and expresses the traits of Kleinfelter's syndrome. If it were an XX sperm cell that fused with the egg, the resulting female offspring would have XXX for sex chromosomes. There's a name for this, but I don't recall it. I believe there is no serious gene expression for this condition, as is the case for XYY. (though there's some debate about violent traits in males with extra Y chromosomes)
On the converse, if there is no sepatation of homologues and one gamete gets both sex chromosomes, you're going to have a gamete with no sex chromosome. If it's a male gamete and it fertilizes an egg (or an X male gamete that fertilizes an egg with no sex chromosome), the sex genotype is XO (or just X), called Turner's syndome. People with this condition are female and do not mature sexually. I don't recall what happens in the YO case, where there's the Y chromosome but no X...I think it results in a nonviable embryo.
That's probably way more than you wanted to know about sex chromosome defects, and I've only touched on a few cases. (incidentally, this post is going to make for an interesting google search result what with the "sex" and "XXX")
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quote:
(incidentally, this post is going to make for an interesting google search result what with the "sex" and "XXX")
Maybe it'll be an education for some people. [:p]
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John - The Eternal Pessimist.
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how do you think i got here in the first place??!!
We don't want the loonies taking over!
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The increasing mental retardation with increasing numbers of X chromosomes (sorry girls, can't argue with the facts !) is not well understood but certainly represents a 'gene dosage' effect. As I said before, even though the extra copies of the X chromosome carried by a cell are inactivated (Lyonised to a Barr body), some genes remain active even on the Lyonised copies. These are the most likely culprits for causing the consequences of extra copies of the X chromosome.
Whilst XO (Turner's Syndrome) results is a viable phenotype, YO (no X chromosome) is inviable.
Extra copies of the X chromosome can arise through the process called non-disjunction and this can occur both during the first, second or both meiotic divisions.
Chris
"I never forget a face, but in your case I'll make an exception"
- Groucho Marx
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Non-disjunction, yeah, that was the word I was digging for. You'd think I'd remember it with finals being next week and all. [:0] At least I remember the process, that's the hardest part.
To add to the original discussion, there is a lot of available space in eukaryotic DNA. I've never read anything making this hypothesis, but surely someone has made the connection is that the extra room allows for us to mutate and acquire new traits that may be helpful in the species survival. Over time, through base substitution mutations, a stretch of noncoding DNA could very well become coding if the correct promoter sequences and stop codons are formed. It's an evolutionary genetic necessity considering we can't just pick up new genetic traits on the fly like bacteria can. Surely there has been some research on this, trying to get eukaryotic cells to develop new coding DNA from a previously non-coding area.
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I think it would be VERY randomly lucky for a total noncoding regoing to aquire all of the parts neccesary for a functional, transcriptionally active gene to form by simple base pair mutations (although evolution occurs in crazy ways) but I believe it happens quite frequently via maechnaisms such as chromosomal rearrangements and transposable elements etc. that can move whole genes, or at least parts of a functional gene into regions where there wan't one before.
It is pretty much accepted that these spaces leave way for eolutionary change, and are likely the reminants of evolutionary change. HOwvwere, where the debate comes in, is why we keep them there over evolutionary time. If they had no beneficial function we would most likely kick out the extra genetic baggage (bacteria will kick out an un needed plasmid, if not selected for my antibiotics, in a few short cell cycles. You pointed out that there is the bennefit of room for evolution, howvere, this hypothisis doesn't exactly hold up because while this IS benneficial, there is no evolutionary mechanism that selects for the future potential to evolve. So the juries still out. There are some very viable hypotheses out there that I've read, but I can't remember any specfics of any of them. I believe if you dig out the issue of Nature that NIH published their draft human genome (Feb 16 2001??) they throw out some ideas in there (somehwhere bedded in the hundreds of pages of that artice, have fun reading) although I'm sure there have been some better theories since then.
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But bacteria have limited real estate as their genome and plasmids occupy a relatively high percentage of cellular space. Our genome is very efficiently packed and our cells are much bigger, we have more than enough room. Since the extra space for genetic information is obviously a benefit, I don't see why we would evolve away from it.
Yeah, there are definately better and faster ways of developing entirely new genes than base substitutions, don't know why I only mentioned that one. Thanks for pointing that out.
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There is more to this than just DNA, the DNA serves a function
to build our bodies and store information, It is a tool of animal life not the source of animal life.
so i thought i'd add a bit to this discussion, and all this
can be backed up with real science, out of the BOX science
CENTRIOLE
The centriole is a small cylinder inside all animal cells, comes with a pair, mum with daughter attached, well sort of floats there next to her, well to tolerances engineers can only dream about, without actually touching, magically :)
in micro gravity experiments in space on animal cells, it's centriole activity that causes most problems, on earth it's centriole activity that causes cancer, in animals it's centriole activity that starts and executes cell mitosis/division, the centriole organises the internal fertilization of an egg. the centriole moves about in the cell where ever it wants, for whatever function. it connects itself up with microtubules to other parts of the cell. DNA is not the intelligence at work, the centriole is. living things interact with gravity more than inert things. living things change in mass, before they die they increase in mass as the quantum process in the centrioles increases to find and answer to the impending death, then when they die they loose mass as the quantum process stops. the centriole is the inertia centre of our cells. is this not evidence enough to start extensive research into the function of the centriole?
animals have centrioles and animals move!!
"if you want quantum computing you don't even
have to look past the end of your nose"
centrioles self assemble a copy of themselves
before mitosis of the cell. this is nanotechnology
if a centriole/s is dissolved inside a living cell it
reforms as if by magic, it doesn't need to copy
itself from another
Microtubules to carbon-nanotubes
Quantum computing - use natures best as a start,
then maybe you might be able to get one to work
And before someone gets smart, and says "neurons don't have centrioles". well when they looked at Einstein's brain, he had normal neuron count but a higher glial cell count, could this be a case of classic mistaken identity because science doesn't have it's missing science of life.
Artcile from Scientific american
http://www.sciamdigital.com/browse.cfm?sequencenameCHAR=item2&methodnameCHAR=resource_getitembrowse&interfacenameCHAR=browse.cfm&ISSUEID_CHAR=3B8A9274-2B35-221B-63A60F782CAB6E84&ARTICLEID_CHAR=3BA32C9C-2B35-221B-63605E90A8809E26&sc=I100322
---------------------------------------------
NOW TO DNA
DNA
The centriole/patterns takes it's DNA with it.
whether this is fertilization of an egg or mitosis/division of a cell, the DNA is taken, it's second, it follows.
" we worry about one mutation in our gene's.
the centriole can mutate our gene's"
adaptive mutation.
J cairns Boston school public health 1985
that says to me
"what ever controls the centriole/patterns controls the mutation of our gene's"
"our body is not as fragile as medicine would have us believe"
"there is something else controlling/causing our diseases"
The DNA is the centrioles/patterns,
toolkit/workshop/manufacturing/warehouse etc.
DNA is what the quantum process
we can't see uses to build the body we can see.
How do we know that there is a quantum process there?
well if quantum computing exists wouldn't life have found it already?
ebz
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but its the protiens encoded by the DNA that make up the centrioles and manipulate their functions.
Jay, I agree with you that we don't have anywhere near as much evolutionary pressure to kick out extra DNA as bacteria do (actually I just learned today that the average is 5 cell divisions or 1 hour for a bacterial cell to kick out a plasmid) but there is still a small pressure against it. I guess that more important point that I was trying to make is that while it is beneficial to have the room for easier evolution, we associate that with a selective advantage, but if you really think about the rules of how evolution and natural selection work, this does not hold up, because there is no way nature can select for "future potential". It has to be a currently manifested trait. I couldn't tell from your post if you understood this or not, so if you did ignore it.
A submarine is NOT a cargo ship!
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a ham sandwhich is a source of portien for our
bodies, are you saying the ham sandwhich is in charge :)
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The DNA that transcribes the RNA that translates the protein is in charge. Centriole formation isn't "magic", it's intermolecular attractions between tubulin proteins.
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quote:
Originally posted by ebzZzZ
a ham sandwhich is a source of portien for our
bodies, are you saying the ham sandwhich is in charge :)
no.... but the DNA that made that protien for the pig it came from was in chage for that pig. When you eat protiens, those protiens don't get used in that form by your body. they get broken down to their amino acids so your cells can make your own protiens out of them (coded by the DNA)
A submarine is NOT a cargo ship!
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read this it does a better job of explaining than
i can
http://rgouin.home.mindspring.com/pdf/reviewB.pdf
and you can't say it doesn't go along way to desribing things
biology ignores, just look at the list of referenced papers.
i think the centriole is going to have the last laugh, but what
this does mean is it's a link between our medicine in the west
and the Qi based medicine from the east, now wouldn't that be nice.
about time the drug companies got whats coming to them and their
shareholders, i know i've worked for most of them, find a disease
to apply a drug for.
ebz
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While I don't agree with that paper's quantum mechanical treatment of a macroscopic system (yes, even centrioles are macroscopic, it would violate heisenberg otherwise since we can observe them directly) I do agree with you that there is a degree of effectiveness in Eastern medicine and that research combining it with western meds that is going on now may yield some effective, cheap treatments. I also agree that drug companies are horrible and well-deserving of comeuppance.
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