ORFans

[sophophilo]

:roll:

problem for common ancestry?

 

[Aught3]

Why did you post this topic?

Anyway, de novo gene evolution is possible. Rare but it happens.

 

[sophophilo]

Why did you post this topic? .

I asked a question... thats not illegal, isn't it?

I've come across this argument and I'm not quite sure how to debunk it, thats all.

 

[Josan]

I have no idea what you are talking about, maybe some more information or a source would be nice?

 

[sophophilo]

I have no idea what you are talking about, maybe some more information or a source would be nice?

Than you may not be the most qualified for an answer to begin with...

ORFans are DNA segements which creationists claim to be a problem for common descent. All I know is that they are not, but I'm not a genius on this field to the extent that I could provide an adequate response.

 

[Aught3]

I asked a question... thats not illegal, isn't it?

Like Josan said, it just seemed weird that you posted no info on what ORFans were, or what kind of answer you are looking for.

 

[Master_Ghost_Knight]

I personaly don't know what the heck ORFans referes to. But I would like to ask that I don't suport common acestry in the literal sense (to a certain degree). I believe that it is more like that several premordial individuals springed out individuality without the necessity for one individual causing the existance of the other. But then only a small group of it would eventualy be sucessfull and give rise to all the species we see today for which you could technicaly say that there is a common descent from one specificorganism (for which a group of original organism could fit this criteria instead of just one and only one).
But sense the result of such an event would be praticaly undestinguishable from the "one and only one common descent", I guess I will never know.

 

[Aught3]

^That sounds like common ancestry to me.

 

[Master_Ghost_Knight]

^That sounds like common ancestry to me.

Does the classification goes all the way there? I don't know I'm not a biologist.

 

[Aught3]

I think you were saying that all life could be traced back to one or a few individuals sometime during the appearance of life. That's basically common ancestry. If you don't accept common ancestry you would have to accept something along the lines of: the bacteria and the eukaryote lineages arose from two separate abiogenesis events, never mixing their gene pools. All life seems to have somethings in common which is why we are fairly sure life can be traced back to a single ancestor or gene pool.

 

[Master_Ghost_Knight]

So I guess it is common ancestry then.

 

[Aught3]

Yeah biology, it's not as strict as math so many fluffy definitions.

 

[Spase]

Yeah biology, it's not as strict as math so many fluffy definitions.

But we're getting better! Definitely though.. still some exceedingly fluffy spots.

On the topic of the OP...

[Edited to remove possibly misleading guesses I made]

I don't have a perfect answer for you because I haven't spent a lot of time looking at ORFans myself. It really is an interesting question...

I can think of some hypothetical answers but they aren't very satisfying. I'll see what I can find to read on the subject, including looking for a few examples. I think if it were something we had a strong answer for we wouldn't still call them ORFans. Hm.

This is why I haven't been around the forum much lately... Doing this is much more fun than what I'm supposed to be working on.. Hah

 

[Spase]

Um.

I have to leave... and I'm not done reading this but it's an interesting paper on the ORFan phenomenon. I especially like the use of scale-free networks to show that ORFans seem to fall into a coherent distribution with other genes.

This is the paper:
http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=2447361&blobtype=pdf

It's title is "Unravelling the ORFan puzzle"

I'll write more useful things when I get time. I haven't finished the whole thing and am still digesting it. The trouble is there isn't a really solid answer, just some hypotheses with shaky supporting evidence. I'm honestly surprised someone who is arguing against evolution knew enough about biology to know what an ORFan even is.

There is an interesting relationship to length such that only something like 7% of ORFans are "long" ORFs. This makes the possibility of rapid evolution much more plausible, and while I haven't had the time to read them, there are published papers suggesting mechanisms and evidence for rapid evolution cited by the paper I linked. Also, that 7% could still be an artifact of incomplete sampling (not enough genomes sequenced to find homologues) or other issues...

Honestly my counter would be "Hey, evolution is useful and predictive. What's your more useful or more predictive theory? What results does it predict?" I'm perfectly fine explaining to someone that science isn't about absolute truth. More often than not it's heuristics that work well enough at modeling the world that we use them and evolutionary theory is just that. Even if evolution was wrong at this point it would be useful in the same way Newtonian mechanics is, we can make predictions from it's models.

Anyway! I hope that was at least marginally helpful.

 

[Aught3]

I like their idea of a model:

Many ORFans may have been generated as the result of a number of possible evolutionary events, which may include horizontal transfer, rapid evolution and gene-loss. ORFans (and other ORFs) without selection pressure have been deleted throughout microbial deletion mechanisms, and thus, microbial genomes are kept at 'reasonable sizes' [43]. ORFans that have retained or acquired an important function are kept, thus creating new sequence families with a seed of a single ORFan.

From this model:

The delicate balance of the rates of generation and deletion is responsible for the maintenance of a compact, clean genome and at the same time, allows the organism to efficiently explore the vast sequence space to generate diversity. The abundance of ORFans and PCOs is merely a consequence of this balance. Any change in the rate of generation/deletion may compromise survival. ORFans are simply the result of a natural evolutionary process and their number is exactly what would be expected from a scale-free system. Thus, in addition to the classical view of 'duplication with modification', the proposed model may be responsible for the enormous microbial diversity.

Interesting ideas, would horizontal gene transfer count as a ORFan though? I thought it had to be a completely new gene which is why I mentioned de novo evolution.

 

[Spase]

Interesting ideas, would horizontal gene transfer count as a ORFan though? I thought it had to be a completely new gene which is why I mentioned de novo evolution.

Funny thing...

Before I edited my first post is I had written something like, "Hmm. Horizontal gene transfer would make sense as long as you're only seeing these in single celled organisms (I'm not aware of multi-cellular critters with horizontal gene transfer)."

I edited because after thinking about it I realized that seemed a bit silly for exactly the reason you suggest. It only makes sense if it was laterally transferred by a species that was later out-competed/went extinct. It's certainly possible but I don't think it could possibly explain all the ORFans. After reading that review I felt a little better but I think it's an incomplete picture and so I didn't want to present it as a clear explanation.

Like I said.. I really like what they had to say in the review... but it's not the sort of stuff that convinces people who aren't interested in really examining the field and are just looking for the slightest suggestion that evolution could have a hole somewhere... But seriously. You don't convince those people anyway most of the time.