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New Virus Paradigm

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Greven:

--- Quote ---NB: Plural of virus is viruses. The forms virii and vira are cases of Hypercorrection.
--- End quote ---

Ah okay, but in danish it is "vira", I just thought that the word "virus" were latin or something (maybe greek), and thus making "vira" the plural of virus in most indo-european language (and especially those that were influenced by latin... (((((although english is not directly influenced by latin, it has some roots in it))))))   )

Who cares? You did understand want I wrote, but I will follow your note. (if I remember it... )

Numsgil:

--- Quote from: Greven ---Who cares?
--- End quote ---

 The biology bourgeois

Elite:

--- Quote from: Numsgil ---Don't have alot of time at the moment to comment, but as I see it you need the mechanism for viruses to be based on the mechanism for horizontal gene transfer.

That is, viruses are more out of control horizontal gene transfered modules than they are something new or seperate.

I'd like to see viruses built on the base of horizontal gene transfer, and not the other way around.

I do like the idea of the transmited codules (viruses, etc.) executing in sync with the main DNA, but there seems to be logistical issues.  Who gets to write to memory first?  How do you decide which of many different viruses/HorizTrannies get to go before or after each other?
--- End quote ---
In answer to your question it would be first-come-first-serve. The viruses that were there first get executed first.

IMHO, Our viruses at the moment are terribly artificial and I would like to see viruses and HGT split up rather than be mismashed into what we have at the moment. I'd rather have an entirely new mechanism for horizontal gene transfer (ie. pumping genes/codules through ties) and scrap the current incarnation of viruses.

Decision time - What do the rest of you think?

When I'm sure I've got a nicely polished system I'll post it as a poll. All I'm stuck on at the moment is the method of 'immunity'.

Numsgil:
I don't like making new systems for every feature we want.  The result always feels a little patchwork.  I'd rather see several related features all emergent from a single mechanism.

This article talks (briefly) about the possible origins of viruses.


--- Quote ---A more widely accepted theory is that viruses are derived from normal cellular components that gained the ability to replicate autonomously.
--- End quote ---

This is the one I personally subscribe to.

As to HGT:
Wikipedia talks about three methods for HGT:

Transformation, Transduction, and Bacterial conjugation.

Bacterial Conjugation most closely resembles passing DNA through ties.  Transduction is what I would consider the origin of viruses in DB to be.  Transduction is passing of genetic material via virus like things.  Imagine such a codule learning to pass itself through Transduction instead of relying on the host.

Transformation is the absorption of random strands of genetic material floating around randomly in the environment.  I don't really see a point in modelling this personally.

Anyway, that's why I'd like to see viruses be an outgrowth of HGT mechanisms.

Elite:
I'm incorporating a basic HGT method into the proposal. It's very similar to the methods in that wiki article. These 'retroviruses' will 'shuffle' DNA around between species.

It's just giving DNA tools to create free-floating pieces of DNA independant from cells.

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