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Scientists Determine Identity, Cell Locale And Quantity Of Nearly All Proteins In An Organism
Science Daily | University Of California - San Francisco ^ | 2003-10-16

Posted on 10/16/2003 4:33:58 PM PDT by sourcery

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To: gore3000
You keep lying about my postings even though they are just above, pretty shameless.

I think I've summarized your arguments fairly. You are, of course, free to differ, and free to say so.

Both mitochondria and chloroplasts can arise only from preexisting mitochondria and chloroplasts.

This is false.

No it isn't; it's completely accurate. If a cell's mitochondria or chloroplasts are destroyed they cannot be reginerated. These organelles are never assembled from scratch. They reproduce themselves within the cell by bianary fission (much like the bacteria from which they are descended). This is why mitochondrial DNA is passed on only from the mother. It is the mitochondria in the egg that reproduce as the fertilized ovum divides and are thereby passed on to the child. (I should say almost always. Very occassionaly a sperm will have some mitochondria -- normally they don't -- and very occassionaly these may be passed on. But the union of these two events is extremely rare.)

If you have evidence of mitochondria arising other than from prexisting mitochondria, then feel free to share it. But you don't because this doesn't happen, and the statement I posted is correct.

Since all eukaryotic organisms have one or the other

Well, you're batting a thousand so far. This isn't correct either. There certainly are eukaryotes that do NOT have mitochondria at all, and some lack chloroplasts as well (for instance the "pelobionts"). Some of them probably branched off from other eucaryotes before mitochondria were acquired, but in other cases there is evidence that mitochondria were lost secondarily (or evolved into relict structures that retain some functionality in supplying genetic material, but don't engage in metabolism of glucose). E.g.:

Direct Evidence for Secondary Loss of Mitochondria in Entamoeba histolytica

Archezoan protists are thought to represent lineages that diverged from other eukaryotes before acquisition of the mitochondrion and other organelles. The parasite Entamoeba histolytica was originally included in this group. Ribosomal RNA based phylogenies, however, place E. histolytica on a comparatively recent branch of the eukaryotic tree, implying that its ancestors had these structures. In this study, direct evidence for secondary loss of mitochondrial function was obtained by isolating two E. histolytica genes encoding proteins that in other eukaryotes are localized in the mitochondrion: the enzyme pyridine nucleotide transhydrogenase and the chaperonin cpn60. Phylogenetic analysis of the E. histolytica homolog of cpn60 confirmed that it is specifically related to the mitochondrial lineage. The data suggest that a mitochondrial relic may persist in this organism. Similar studies are needed in archezoan protists to ascertain which, if any, eukaryotic lineages primitively lack mitochondria.

and this is an essential function without the cell cannot survive they are an integral part of the eukaryotic cell.

Better. This is true as a rule of thumb -- as I've said, no one denies that modern mitochondria are highly integrated into the cell -- but it is false at the specific level because there are: 1) eucaryotes that get along quite well without mitochondria and/or chloroplasts (see above) and, 2) because in some heterotrophic protists mitochondria can be eliminated without harming the cell (granted these have chloroplasts).

these genomes are very small and cannot and could never have provided the essentials of life for any individual organism. [paragraph] The other similarities again do not speak to the problem that these could never have been individual organisms.

Of course they could not, as they exist now, but then this is a strawman. The endosymbiotic theory holds that the ancestors of mitochondria were intially engulfed as free living bacteria (there are plently of contemporary examples of this, btw) and then, over time, became symbiotic with their host, possibly starting out as parasites (there are also modern example of this happening), and then, again over time, developed the tight, integrated and obligate relationship we see today.

In short there is no evidence that these chloroplasts and mitochondria were ever anything but what they are now.

Like I said: bald assertion and sheer denial. The evidence is there as summarized. You are simply asserting that it couldn't happen, but all at least of the initial stages required by the endosymbiotic theory -- engulfment of one cell by another with the engulfed cell surviving and continuing to function and reproduce, the development of the engulfed cell into a parasite, the evolution of parasites into beneficial symbiots, the evolution of faculative symbiots into obligate symbiots -- have actually been observed to occur in modern examples.

41 posted on 10/18/2003 8:48:57 PM PDT by Stultis
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To: gore3000
The only reason for this totally factualless assumption by atheist/evolutionists is that the theory of evolution requires it.

Ooops. Another false statement. Sorry, but there were so many I overlooked this one. No, this theory is not "required" by evolution. How the heck do you figure that? The endosymbiotic theory is of fairly recent origin. Off the top of my head I believe it was first suggested (but never tested or developed into an actual theory) in the mid-20's or thereabouts. It was only developed as a serious theory in the last twenty years (if IIRC), and generally accepted even more recently.

The mitochondria and cholorplasts developed from symbiots is only the way (apparently) that it happened to work out. There is nothing in the theory of evolution that requires that it happened this way. Similar organelles might have been evolved within the cell, or their functions might have evolved in some other way. After all bacteria evolved them in the first place.

42 posted on 10/18/2003 8:57:28 PM PDT by Stultis
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To: Stultis
I think the simple answer is that the evolution and development of the mitochondria preceeded the evolution of the cell wall.
43 posted on 10/18/2003 9:20:48 PM PDT by djf
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To: Stultis
these genomes are very small and cannot and could never have provided the essentials of life for any individual organism. [paragraph] The other similarities again do not speak to the problem that these could never have been individual organisms.-me-

Of course they could not, as they exist now, but then this is a strawman. The endosymbiotic theory holds that the ancestors of mitochondria were intially engulfed as free living bacteria (there are plently of contemporary examples of this, btw) and then, over time, became symbiotic with their host, possibly starting out as parasites (there are also modern example of this happening), and then, again over time, developed the tight, integrated and obligate relationship we see today.

Fact remains that regardless of the rhetoric the production of ATP is necessary. The endosymbiotic theory has absolutely no factual evidence behind it as you admit above. For it to be true both the prior ATP mechanism had to have dissappeared without a trace in all these organisms, the new parasitic organisms had to have reduced themselves (all of them the same way! in all organisms!) to unviable organs, and all examples of these original parasites must have dissappeared from everywhere. All of this shows my point quite well - that this is garbage, it is fact-free pseudo-science and there is no evidence for it except the need of evolution to make up a story to justify its theory in this very important and essential part of living organisms.

So what this discussion comes down to (which you will strenuously deny) is that my original statement is absolutely true - mitochondria and chloroplasts are original organs of eukaryotic organisms, just like many other organs in these organisms are original with them and cannot be claimed to have arisen as parasites. There is no evidence otherwise and the 'endoplasmic theory' is just more evolutionist made up nonsense.

To further complicate the problems that mitochondria create for evolutionists it should be noted that unlike other DNA, the genetic code of mitochondrial DNA is not only different from that of normal DNA but it also differs between species! Fredrick Sanger 1980 Nobel Lecture. So just more proof that this was not a parasite.

44 posted on 10/18/2003 9:55:08 PM PDT by gore3000 ("To say dogs, mice, and humans are all products of slime plus time is a mystery religion.")
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To: gore3000
The endosymbiotic theory has absolutely no factual evidence behind it as you admit above. For it to be true both the prior ATP mechanism had to have dissappeared without a trace in all these organisms,

Huh? I could be wrong, being far from expert on these matters, but as far as I know all eucaryotes that lack mitchondria only produce ATP anaerobically, nor am I aware of any evidence that eucaryotes ever had the ability to produce ATP aerobically apart from mitochondria. And of course eucaryotes all retain the ability to produce ATP anaerobically. So what it is that you are saying "had to have dissappeared without a trace" is a complete mystery to me.

45 posted on 10/19/2003 12:50:06 PM PDT by Stultis
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To: gore3000
So what this discussion comes down to (which you will strenuously deny) is that my original statement is absolutely true - mitochondria and chloroplasts are original organs of eukaryotic organisms

Yes. It comes down to this bald assertion on your part. That's what I've been saying!

46 posted on 10/19/2003 12:53:02 PM PDT by Stultis
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To: sourcery
Recognizing that it is the gene's products -- the proteins that interact to regulate all life processes, many researchers have begun to turn their attention from the roster of all the genes in an organism - the genome -- to the proteome.

This is good, because the genome is what the proteome uses to get its job done. The genome, which has before been called the master molecule of life, is entirely passive. Even its structural and informatic integrity is maintained by proteins.
47 posted on 10/19/2003 12:59:15 PM PDT by aruanan
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To: Stultis
And of course eucaryotes all retain the ability to produce ATP anaerobically. So what it is that you are saying "had to have dissappeared without a trace" is a complete mystery to me.

Yes, all eucaryotes can produce ATP through glycolysis, but this is very inefficient and is doubtful whether eucaryotes could have arisen without the more efficient energy systems provided by chloroplasts and mitochondria.

This still leaves the following problems for evolutionists totally without explanation:

1. the destruction of all freely existign chloroplasts and mitochondria. (the dog ate the homework)
2. the destruction of their ability to exist as self sufficient entities once they were supposedly taken over by eukaryotic organisms.
3. Why the mitochondria of all surviving organisms lack the same abilities of self-sufficient survival in all species.
4. Why there is no stepwise loss of abilities in even the most primitive species.
5. Why mitochondria and chloroplasts require products and proteins from the rest of the eukaryotic organism to perform its functions. (here it should be noted again that it is the same proteins and products in all species that are needed and that of course without all this in place the chloroplasts and mitochondria would have been a deleterious addition to the organism and thus selected against).
6. The problem of differing genetic codes in the mitochondria of different species is totally inexplicable in any evolutionary manner.

What all this shows again is that there is absolutely no evidence for the evolutionist assumption that mitochondria and chloroplasts were self-sufficient organisms at one time which became part of eucaryotic organisms through endosymbiosis. So my statement that this is just another factually empty assumption of evolutionists which is contradicted by strong observable facts is correct.

48 posted on 10/19/2003 9:40:30 PM PDT by gore3000 ("To say dogs, mice, and humans are all products of slime plus time is a mystery religion.")
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To: gore3000
Your list of "problems" aren't cogent objections to the endosymbiotic theory; they simply amount to assertions that evolution can't occur, and we already knew you believe that. Some your "problems" are downright silly, e.g.:

1. the destruction of all freely existign chloroplasts and mitochondria. (the dog ate the homework)

Obviously chloroplasts and mitochondria don't live idependently. No one suggests they do, and certainly no theory suggests they should, or could. Their ancestors lived freely. At a purely logical level, this objections is like claiming that you couldn't possibly have descended from your great-great-grandfather because he's no longer "freely existing".

49 posted on 10/19/2003 10:49:16 PM PDT by Stultis
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To: gore3000
Yes, all eucaryotes can produce ATP through glycolysis, but this is very inefficient and is doubtful whether eucaryotes could have arisen without the more efficient energy systems provided by chloroplasts and mitochondria.

No, not only is it not "doubtful," it's most certainly possible, because there are eucaryotes alive today that manage without either!

50 posted on 10/19/2003 10:53:42 PM PDT by Stultis
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To: gore3000
6. The problem of differing genetic codes in the mitochondria of different species is totally inexplicable in any evolutionary manner.

I don't understand why you think this is so. It seems to me it would be more inexplicable (from an evolutionary perspective) if they were all the same. Remember that mitochondrial DNA evolves too, and seperately from the nuclear DNA. (In fact, I would think it should evolve faster, all things being equal, since it lacks some of the more advanced DNA repair mechanisms operative in the nucleus.)

51 posted on 10/19/2003 10:59:59 PM PDT by Stultis
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To: gore3000
Mycoplasma pneumoniae is one of the smallest bacteria known with a cell diameter of about 0.5 mm

Half a millimeter? That would make it visible to the human eye.

52 posted on 10/19/2003 11:02:44 PM PDT by Timesink
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To: gore3000
5. Why mitochondria and chloroplasts require products and proteins from the rest of the eukaryotic organism to perform its functions.

Why is this such a problem? Never heard of DNA transformation? There's a little field called "genetic engineering" that's based on it. Bacterial DNA gets worked into eucaryotic nuclear DNA all the time. Usually by viruses, but IIRC there are also documented cases of this happening when bacteria are engulfed.

All that's required to get mitochondrial DNA into the nucleus is for a mitochondria to degrade in the cytoplasm, and for some of its DNA to get trapped in a vacuole and transported to the nucleus. This is no very big deal.

53 posted on 10/19/2003 11:07:06 PM PDT by Stultis
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To: Timesink
Mycoplasma pneumoniae is one of the smallest bacteria known with a cell diameter of about 0.5 mm-article quoted-

Half a millimeter? That would make it visible to the human eye.

When I pasted the quote for some reason the greek mu was turned into an m.

54 posted on 10/20/2003 4:59:12 AM PDT by gore3000 ("To say dogs, mice, and humans are all products of slime plus time is a mystery religion.")
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To: Stultis
Let me deal with your various posts as one:

1. Obviously chloroplasts and mitochondria don't live idependently. No one suggests they do, and certainly no theory suggests they should, or could.

That's what you have been arguing from the start, that they were parasites and hence were individual organisms which were captured or intruded themselves into eukaryotic organisms and entered into a symbiotic relationship with them. The above is an admission that I am correct and your argument all along has been false. Thanks for being truthful.

6.I don't understand why you think this is so. It seems to me it would be more inexplicable (from an evolutionary perspective) if they were all the same.

Pretty simple really. What the genetic code does is it translates from the DNA to the amino acids used to make proteins. To change the genetic code successfully without killing the organism and totally destroying functioning you have to do two things - change the DNA code in all the proteins and change the way the code is read into amino acids. You thus need two things to happen at once and of course that is impossible to do gradually.

5. Why is this such a problem? Never heard of DNA transformation? There's a little field called "genetic engineering" that's based on it. Bacterial DNA gets worked into eucaryotic nuclear DNA all the time.

Well, that's the problem with your answer "Bacterial DNA". Yes bacteria can grab DNA from other bacteria and it is often done experimentally BUT EUKARYOTES ARE NOT BACTERIA and do not do that and such has never been observed. So you are getting desperate. First you had said they were free-living parasites, now you see such cannot be said so you pull this from bacteria which does not apply. Methinks you have lost the point pretty decisively.

In addition to having refuted your counterarguments decisively three of my arguments which are also pretty decisive you were unable to respond to:

2. the destruction of their ability to exist as self sufficient entities once they were supposedly taken over by eukaryotic organisms.
3. Why the mitochondria of all surviving organisms lack the same abilities of self-sufficient survival in all species.
4. Why there is no stepwise loss of abilities in even the most primitive species.

So, regardless of your rhetoric, I have proven my point quite well that this endosymbiosis of mitochondria and chloroplasts is just more evolutionist nonsense and more fact-free pseudo-science from people who really should know better.

55 posted on 10/20/2003 6:49:42 PM PDT by gore3000 ("To say dogs, mice, and humans are all products of slime plus time is a mystery religion.")
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To: gore3000
Well, that's the problem with your answer "Bacterial DNA". Yes bacteria can grab DNA from other bacteria and it is often done experimentally BUT EUKARYOTES ARE NOT BACTERIA and do not do that and such has never been observed.

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

You are DEAD wrong (again). Any decent molecular biology text book will cover the topic of "transformation" in eucaryotes (including animals). Heck, you can get genetic material (including bacterial genes) into animal nuclear genes simply by microinjecting naked DNA into the nucleus. You don't even need a plasmid or virus.

I'm afraid I don't see the logic behind any of your other points, so I'll let them be.

56 posted on 10/20/2003 8:22:13 PM PDT by Stultis
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To: Stultis
You are DEAD wrong (again). Any decent molecular biology text book will cover the topic of "transformation" in eucaryotes (including animals). Heck, you can get genetic material (including bacterial genes) into animal nuclear genes simply by microinjecting naked DNA into the nucleus. You don't even need a plasmid or virus.

You can do a lot of things in the lab, but it does not happen in nature. Yes, they do all kinds of genetic engineering on plants and animals, but it does not happen in nature. Only bacteria exchange DNA, eukaryotes do not. Your desperation is getting pretty blatant. As I said from the start, this is another evolutionist tall tale based on nothing except the need for evolutionists to try to talk away strong proof against their theory. In most places it is called bs.

57 posted on 10/21/2003 4:48:11 AM PDT by gore3000 ("To say dogs, mice, and humans are all products of slime plus time is a mystery religion.")
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To: Stultis
Placemarker
58 posted on 10/23/2003 10:02:01 AM PDT by Ogmios (Since when is 66 senate votes for judicial confirmations constitutional?)
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