Problems with Chromosomal Evolution - From Circular to Linear

I don't think it is a red herring, it is integral to some things. Here is an (exagerated) example: There is a certain protein composed of 100,000,000 amino acids, and it is somehow known that it could not have evolved in more than 1 generation (I am not claiming the stuff with telomeres is near that, this example is hugely exagerated). What would that make you think about evolution, and why? But in cells there is not a simple gradient from simple to complex - an enzyme either works or it doesn't. Natural selection sees no difference between "not working" and "almost working." Enzymes are hurdles - they cannot be taken by small amounts; the whole thing has to be cleared in one jump. I'm aware of that. Exactly - and I think that the systems in question couldn't have gotten from non-existent to working, and would have been discarded.

Are you sure about that? It seems to me that since all enzymes do is reduce the activation energy of certain chemical reactions, there could easily be a complexity gradient - i.e. you might have two enzymes with active binding sites for the same molecules, but one of them is able to catalyze the reaction at a lower activation energy than the other.

quote:

---

But in cells there is not a simple gradient from simple to complex - an enzyme either works or it doesn't. Natural selection sees no difference between "not working" and "almost working." Enzymes are hurdles - they cannot be taken by small amounts; the whole thing has to be cleared in one jump.

---

And this sort of jump has been observed. Take the nylong bug, for example. A one base insertion caused a frame shift that resulted in a functional enzyme that cleaved one of the byproducts of nylon production (reference). So actually new enzymes with novel activity are able to arise in a one-time mutational event. You are correct in stating that natural selection can not select between "not working" and "almost working" (which are actually the same thing) but it can select against "suddenly working" and "not working".Given this example, it is quite possible that the first telomerase could have arisen from one single mutation that was not planned and accidental just as we have observed in the nylon bug.

True, once an enxyme is working it could be improved on (although for most enzymes I'm guessing it would take large changes to change anything and keep it functional). But the step from functional to non-functional protein or enzyme is what I was talking about when I said "hurdle."

This is another thing I'll have to research. I'm still working on your other post about t-loops, I'll post a reply to that soon-ish (I think).You guys sure have a knack for making me spend inordinate amounts of time researching. Probably a standard evilutionist tactic...

Right, but that's a lot less of a hurdle than you made it out to be if there's varying levels of functionality.

Immediately? Tomorrow? Next week? What is the time frame here? What kills it? There will always be some molecules available inside the cell that may be added to the end of the chromosome as it tries to close\repair itself ... what happens when one holds it together just enough ... Implausible is not impossible.Why does it have to be DNA? We are talking the first replicating cell system and the environment then was totally alien to what we live in, the chemical energy system was different. Latest thought is that RNA could have just as easily been the best replicator before DNA evolved from it, perhaps there was a simpler but less effective molecule before that. The LUCA project is trying to determine just how little\simple the replicating molecule needs to be.Why do you assume it stopped being needed? If circular chromosome breakage was common a stabilizing system could be maintained and even improved with time to hold things until circularity was re-established. Perhaps they are the molecules that first caused the circular chromosome to close, that becomes a repair molecule, that gets damaged while not needed but then employed in a new way ...... and a molecule that was needed from time to time could then be fatal to the ones that lose it and then break open.Certainly a linear molecule is simpler than a circular one, so evolution and probability would tend to favour the linear system first. A crude inaccurate system with a high degree of failure would still out compete pure chance combination of amino acids -- remember it does not have to be as good as the system today (in a different environment), it just needs to be good enough.and the issue of improbability has been addressed on other threads -- think of a lottery: highly improbable that any one specific ticket will win, highly probable that one of all the tickets will win ...
see http://EvC Forum: the old improbable probability problemand if it did "just happen" then the improbability is irrelevant.enjoy.

---

we are limited in our ability to understand
by our ability to understand RebelAAmerican.Zen[Deist
{{{Buddha walks off laughing with joy}}}

Harking back to a previous thread concerning early life (about the origin of viruses):What if the origin of the nucleus is a complex viral genome that got 'stuck' in a primitive archaea? That way, a linear genome (in the early pool of proto-cells) could be replaced by a circular one (in Archaea and Bacteria), which in turn got usurped by a more stable linear model (to produce an early eukaryote).This is a paper suggesting just that (I think, I can't get access to the full text).I don't know if the article is much cop, because I can't read the full text and its's only a 'comment' or 'letter'. I also have no idea whether it has been laughed at by all and sundry since then, but here's a snippet from the abstract:

quote:

---

It is proposed that several characteristic features of the eukaryotic nucleus derive from its viral ancestry. These include mRNA capping, linear chromosomes, and separation of transcription from translation.

---

Any thoughts?

Hmmm a DNA viral mechanism could also hark back to a more primitive organism overshadowed by later evolved more complex cells. Certainly by the time we are talking about developing eukaryotes, life has been around for a while.This talks about the first predator engulfing others for raw materials, while the viral model is to enter the 'prey' and attack\co-opt from inside? This also leaves the original outershell as camoflage in case of colonies.Other papers have suggested a lot of DNA\RNA interchange between early cellular organisms. A form of group sex?These viral remnants would still have already developed the capping\telemere solution by this time as well. Thus this does not solve our OT problem.One thought this brings to the OT problem though is that dead and dying cells would be consumed by others, cells that had broken circular chromosomes could be incorporated, and in the process get combined with other remnants, one becoming a cap for another.interesting thoughts.Going off on a tangent I posit that a virus entering a cell is similar to a sperm entering an egg ... perhaps this mechanism is behind the evolution of sex (once a symbiotic relationship has become established)? The idea of males as viruses would, I'm sure, amuse many. Could be an interesting new topic?

---

we are limited in our ability to understand
by our ability to understand RebelAAmerican.Zen[Deist
{{{Buddha walks off laughing with joy}}}

quote:

---

These viral remnants would still have already developed the capping\telemere solution by this time as well. Thus this does not solve our OT problem.

---

The host cell could use the viral long tandem repeats (LTR's) through retrotrasposition to solve the problem of end deletion in linear DNA replication. A similar mechanism is used in Drosophila, although the whole viral genes are used instead of LTR's.

has anyone tried to remove the end caps from straight chromosomes and see if a protection system evolves?are there molecules that cause circular chromosomes to open, and are they catalytic or do they combine in the process?

---

we are limited in our ability to understand
by our ability to understand RebelAAmerican.Zen[Deist
{{{Buddha walks off laughing with joy}}}

quote:

---

has anyone tried to remove the end caps from straight chromosomes and see if a protection system evolves?

​

are there molecules that cause circular chromosomes to open, and are they catalytic or do they combine in the process?

---

There are some tantalizing hints that this work has been done, but I haven't been able to find free access to any of the primary literature as of yet.From The Rockefeller University » testpost for LDAP authorlogin : And from de Lange's Rockefeller university page The Rockefeller University : (this is just a snippet, the whole description is worth a read) de Lange seems to be the most active researcher on the evolution of early telomere systems and human telomere control, at least during my brief searches. I have found some of her papers but they are not free-access. I could order through my job, but it really wouldn't be that ethical.I will keep looking, but I thought it might go faster if two people were looking down the same path. If anyone else has access to more of de Lange's work feel free to post it here.

Everybody,
I'm leaving on a two week or so vacation in a couple days, so this'll be my last post for a while. When I get back I'll keep researching all the arguments, and hopefully soon after my return I'll start rebutting them.Later,
JT

OK. We'll try to keep it down to a dull roar so theren won't be too much to cover.You may want to bookmark your last post on this topic so you can get back to it even if it has dissappeared from the radar?

---

we are limited in our ability to understand
by our ability to understand RebelAAmerican.Zen[Deist
{{{Buddha walks off laughing with joy}}}

Thanks, I will. Although having your guys' arguments floating around in my head for two weeks without my having a rebuttal is going to drive me nuts...Also, you guys can post as much as you want in this thread, the more the better. I'll just start where I left off and work through it. (I appreciate your consideration, though.)Later,
JT