maybe I am doing history - the first response from ITALY ... (trip)

Avinatan, please, leave behind these subjective terms as "positive", "negative" & "useless" , it has nothing to do with reality, just with a narrow point of view.
proteins are nor posetive or negative, they are in all spectrum in between, from most needed, to not-needed, and it depends on the situation .
as I said before, there is NO meter for the usefulness of a protein, so I really don't know where you get these ideas about "no useless proteins" - no such thing.
the beauty of life is this, and mark my word : life procedures are NOT efficient, they tend to be inefficient (replication, translation, photosythesis). this is VERY efficient in the long-run, since the unexpectable state of the enviroment picks up the most suitible resolution , one that was "invented" in random.
life has no plan , it scatters in random, the best wins.

My fundamental question is do exist proteins in the
body which have no effect on body function

I think that evolution of trial & error makes the existence of many such proteins a necessity

'They are inevitable products of that 'error

we almost agree, but not.
functionless proteins? yes , I guess it could be (but protein killers like ubiquitin will trash most of them)- but, be carful not to mix "functionless" with "useless".
and I will explain:
even a "usless protein", one that has no catalitic function, has an effect, how so?
it may bond to other cellular components, or aggragate in the cell (usually it is bad news for the cell), or change the osmotic tension by its sear existance.
you see, no free meals and easy answers in biology.
there are no inert proteins.
they all count.

about the other part, i must compleatly disagree.
unless we are talking about a strees enviroment, exposure to hunger (and so on), I believe the body (or selection, if you want) will NOT minimize the energy loss of these "functionless proteins"
we are very enrgy wasting.
that is the fundemental differance between a human made machine and a nature made machine- nature, unlike us, does leave loose-ends in it's creations

at last, we agree!
it will be reasonable to essume there are redundent copies of a gene.
in fact, we know there are, the phenomenon of redundancy of genes, and of metabolic pathays is well documented.
also, the existance of pseudo-genes (mentioned in this talk many times) is a indirect proof for such redundencies ,
as they used to be genes, but the body tolerated their loss of function (because they had doubles).
another point to take in mind is the regulation of expression, mainly feedback-inhibition, which means the more protein is created, the less it will further be created.
in this kind of regulation, the original amount of proteins will stay the same even if the body will make duplicates of the gene.

if I may diagnose you for a second,
your problem is not with the lack of knoladge, but in your rigid concepts, which you continiusly stick to : good-mutatuions, bad-mutations, ussless-proteins, and so on.
these are all simplifications, the data we knowy shows us that they are all ralative and not constants..

Avinatan, if I understood corectly, you are a medical doctor.
if so, I have for you an example that should be femiliar, and it will show you the vast use of randomness in the body.
The immune system.
How is the body capable of fighting new pathogens it never has exposed to before?
Does it relay on "genetic knowladge" of the pathogens? - NO.
Does it depend only on the unlearning innate system, like plants do? - NO.
and most important,
Does the body analys the menis, the cause of illness, and then creats the cure? - NO.
This is a fundemental principal:
not a plan or a will is the driving force, but random, blind guesses, by the body.
Our immune system, for all its capability and diversity, is all derived by randomly created proteins, namly : antibodies and MHC receptors.
This is a fine example of the complexity and "wisdom" that may origin from random.

another example , from the field of phisics is the whole notion of CAOS.
complex fractals and beautiful patterns (like life?) may be created with very few forces.

hay! we are both online - cuwl!
guys,
every area in italy has different cookings and kitchen.
so "italian food" is an invention of us, non-italians...
: )
In the north they have the most stupid bread-bans, the intefada shabab can use them as rocks (that hard).
The food in toscana is a dream (damn, I sound like ron meybarg..), and sicily's cakes with all their sugar covers are the best.

bon epetit

You are quite right. I'm a physician.
I have always thought that the development of the immune system and the 'random' creation of billion antibodies against every possible antigen in the world are a very good model of the evolution. However, in this case we ought to find many harmless and useless proteins exactly as each of us have many antibodies which would never be used.
Therefore, the publication in the science, which argued that the proteins of the live creatures are very few comparing the diversity and complexity of the biology had driven me to seek other explanations.

A second point, Do you really think that the somatic mutations of the Limphozites which are responsible for the creation of immune system were a result of random process ? That phenomena seems to me too much sophisticated.

as for this "lack of usless proteins" argument, I believe I replied on it previously.
if thae immune system is derived from random - what does that tell you about nature and the use of random?

yes, I do.
(until other proof will show up)

. Thank you for your interesting answers. Further questions would clarify the issue. 1.Duplications mutations which stil are not "advantageous" would appear only in a small section of the population, Have you examples for such "poly morphisms" which are probebly waiting for point mutations.?
2.Assuming that A.C.T.H. developed from a duplicature of the gen of M.S.H. also M.S.H. receptor should have been converted to A.C.T.H. receptor. Why the D.N.A. of this new receptor would be expressed only in the adrenal tissue, where it is usfull, and not in any other tissue?
3.There are about thirty thousands protein produsing gens in the humen being, but ten trilions anti bodies due to spontaneous somatic mutations in the iymphocytes .Why shuch somatic mutations are observed only in the Igv section of the lymphocytes , and not any where else? I would be very thankful for your answers.

alternative splicing

.. that this interpretation is faulty. I don't think that the cat is in a superposition until he is contaminated with a human observer - the cat itself is the observer, and it's already dead, or not.

In any case, once I've studied Quantum Mechanics a bit, I'll tell you which interpretations makes more sense to me. As it is, I don't know enough about it to choose any of the other interpretations.

E=mc^2