Giardia Bares All: Parasite genes reveal long sexual history

Science News Online ^ | Jan. 29, 2005 | Christen Brownlee

[Ichneumon]

If we have a fast-changing bacteria, say 100 alleged "mutational events" per day, would 4 billion years be long enough to see some unused code get filtered out?

Probably not, no, since organisms have more of a vested interest in making sure they faithfully copy their DNA (which necessitates accurately copying even the "fluff", since it can't "tell" the difference), than they do in error-prone "snippage" which under most circumstances provides a very negligible advantage.

In short, the risks of "losing" parts of the DNA outweigh the possible benefits, so organisms have an evolutionary incentive to maximize their reliable DNA preservation and copying (even when that includes copying garbage as well as the critical genes).

Short form: Yeah, there may be a *slight* evolutionary pressure to "clean" the genome, but there are *other*, *stronger* evolutionary pressures to leave a working genome alone and intact as much as possible.

Furthermore, while some junk DNA will (and does) drop out by "lucky" random mutation, more keeps getting made via other random mutation, so there will be no long-term trend towards "genome cleaning".

[Ichneumon]

a single-celled parasite has been ready for sex for billions of years.

I think we can *all* relate to *that* feeling...

[xm177e2]

If we have a fast-changing bacteria, say 100 alleged "mutational events" per day, would 4 billion years be long enough to see some unused code get filtered out?

If the code really is completely unused, and the genetics are rapidly changing, you might expect it to get lost in the shuffle, yes. But DNA that isn't out-and-out harmful is hard to get rid of, and there's always some new "junk DNA" to take the place of the old stuff. Junk DNA just doesn't put a high enough cost on the cell for it to be selected out quickly. At least, that's one possible explanation. I haven't studied it, so I couldn't tell you for sure.

There are more ways for junk DNA to get into a cell than for it to be lost. For instance, some viruses will pick up other bacterial DNA instead of virus DNA by accident before leaving a host cell; when they attach to some other cell, instead of infecting it with viral DNA, they add in part of the DNA from the cell they just left. There's all sorts of crazy ways for bacteria to pick up junk DNA (or useful DNA).

[Southack]

"Finally, coming full circle on this discussion -- if our genomes were "designed", why did the "designer" put so much useless junk into his work?"

Have you ever looked at large, long-lived software projects such as MicroSoft Windows? Enormous amounts of old, unused code is copied due to lazyness and reducing risk (Oh gee, Bill...we thought that subroutine wasn't used any longer), as well as currently unused code that is inserted or left for "hooks" to anticipated future software. Such projects also tend to leave in some benchmarketing and profiling routines, useful only to the software designers, simply because removing such code would require re-testing before deployment.

"On the other hand, accumulating harmless random junk is exactly what one would expect from evolutionary processes..."

Yes, but here's the rub...we see neither of the two things that we would expect from an unaided, purely Evolutionary system in our currently sequenced genomes.

We would *expect* to see DNA junk code incrementally increase in *every* later species...or else we would expect some genetic mechanism to gradually filter *all* of the junk DNA code away.

We see neither. Some newer species like the Fugu have very little DNA junk code, while some older bacterias have large amounts of junk DNA (while brewers' yeast has very little).

So the junk DNA jumps around. It neither incrementally increases in each newer species, nor does it gradually get incrementally filtered out.

That should be RINGING LOUD ALARM BELLS among serious students of Darwinism.

[Southack]

"There are more ways for junk DNA to get into a cell than for it to be lost. For instance, some viruses will pick up other bacterial DNA instead of virus DNA by accident before leaving a host cell; when they attach to some other cell, instead of infecting it with viral DNA, they add in part of the DNA from the cell they just left. There's all sorts of crazy ways for bacteria to pick up junk DNA (or useful DNA)."

So shouldn't we see more junk DNA code in all older species?

[AntiGuv]

This is false:

Natural Selection *should* favor those without the unused code...

Natural selection does not favor those without unused code. Natural selection favors the survival of the fittest. If the G. intestinalis with unused code is the fittest in its ecological niche, natural selection favors its survival. If a G. intestinalis emerged without unused code, natural selection probably wouldn't much care, at least in the short term. It would almost certainly be a neutral trait for survival/procreation.

In the long term it's an open question which one would be favored, because it depends on which one could more effectively adapt to whatever competitive pressures might then arise. If the absence of unused code made the G. intestinalis less capable of adapting, those versions would not be favored by natural selection (if adaptation were required). If the presence of unused code made those other G. intestinalis less capable of surviving, then they would not be favored (if resources were sufficiently limited). And so on.

But your basic statement is simply false. In the absence of competitive pressure, natural selection is merely survival of the adequate...

[Southack]

"This is false: Natural Selection *should* favor those without the unused code..."

Don't take my word for it, please see Post #98.

[Doctor Stochastic]

...if our genomes were "designed", why did the "designer" put so much useless junk...

Perhaps She's just a slattern? (Or a packrat.)

[Southack]

c#104

[AntiGuv]

Ichneumon was kind enough to think that he could respond without spelling every detail out; I realized that was not the case.

PS. I did read his post before I replied. Feel free to read his post again and identify where it actually disagrees with mine.

[Ichneumon]

There are more ways for junk DNA to get into a cell than for it to be lost. For instance, some viruses will pick up other bacterial DNA instead of virus DNA by accident before leaving a host cell; when they attach to some other cell, instead of infecting it with viral DNA, they add in part of the DNA from the cell they just left. There's all sorts of crazy ways for bacteria to pick up junk DNA (or useful DNA).

Another example: The human genome permanently contains roughly *20,000* (not a typo) different sections of "fossilized viruses" (known technically as ERVs, or Endogenous RetroViruses). These are relics of failed viral infections which took place in our long-ago ancestors and then passed down to us in our DNA.

Retroviruses are a class of viruses which reproduce themselves by actually inserting their own DNA "inline" into the genomic DNA of the infected host. Normally the viral reproduction cycle then kills the cell so infected, but at times a virus will "fumble" the insertion and just leave a "broken" copy of itself permanently stuck in the host's DNA. If this happens to occur in a cell in the host's germ line (like a sperm or egg cell, or the cells which produce sperm/eggs), then the inactive virus "stuck" in the DNA will be *inherited* by the resulting offspring and be found in the DNA of *all* of his/her cells. And then subsequently passed along to each subsequent generation ad infinitum.

Here's the really fun part: lots of the ERVs in our DNA were not originally contracted by one of our human ancestors, but by one of our PRE-HUMAN ancestors. How do we know this? Because the exact same ERVs (same basepair sequence, same "fragmenting", exact *same* basepair insertion point) are found in various *non-human* genomes, indicating that both lineages inherited that specific ERV from a COMMON ANCESTOR, before the evolutionary split which eventually resulted in humans and the other species.

Here, for example, is the "map" of some of the ERVs found in humans which are also found in various other groupings of primates:

(Each labeled arrow on the chart shows an ERV shared in common by all the branches to the right, and *not* the branches that are "left-and-down". This is the pattern that common descent would make. And common descent is the *only* plausible explanation for it. Furthermore, similar findings tie together larger mammal groups into successively larger "superfamilies" of creatures all descended from even earlier common ancestors.)

Notice how the pattern of "shared nesting" based on shared ERVs *alone* just "happens" to look exactly like the branching ancestry pattern which evolutionary biology arrived at by other lines of evidence... What a "mere coincidence", eh?

[Southack]

"Feel free to read his post again and identify where it actually disagrees with mine."

Post #98 says that you and I were both correct on our earlier points. In contrast, you claimed that I was spreading a falsehood.

Post #98 says that what I posted was no falsehood.

[Southack]

"And common descent is the *only* plausible explanation for it."

No, there are other plausible explanations. Code fragments in computer software can be found in widely different applications, for instance (e.g. MS Word, MS Excel), yet we KNOW for a fact that MS Word and MS Excel were designed "intelligently," not evolved unaided.

Another plausible explanation is simply that species caught the same viri on their own. It's not outrageous to think that both a monkey and a human caught colds or got infections in open wounds...acts that have nothing to do with any purported "shared" ancestry.

[AntiGuv]

Fair enough. I will take the liberty of rewording his statement to fill in the blanks.

Southack is correct to the extent that selection favors "trimming" unused junk from the genome in the very rare cases where the tiny amount of extra energy required to copy "junk" DNA (relative to the far larger ordinary metabolic demands of an organism) becomes a "make or break" issue for a given organism -- and it seldom is. However, AntiGuv and furball4paws are correct in that the amount of selection would in actuality be *very* slight, and that ordinarily evolution would not be expected to seriously "prune" genomes, except in the very rare cases where the tiny amount of extra energy required to copy "junk" DNA (relative to the far larger ordinary metabolic demands of an organism) becomes a "make or break" issue for a given organism -- and it seldom is.

That should connect all the dots for you. If Ichneumon believes I have misrepresented his statement, then he's welcome to correct me for my uppityness. ;)

[Southack]

Thanks. That's fine. It's nice to not be hammered for spreading a falsehood...especially when I didn't spread one, so thanks for the correction.

Now, with that out of the way, if there is such miniscule evolutionary pressure to trim out junk DNA code, and if there are so many ways for junk DNA code to be introduced, should we see a predictable *pattern* in the accumulation, in the same species, over time, of junk DNA code?

[Ichneumon]

Don't take my word for it, please see Post #98.

...and be sure to read *all* of post#98, which goes on to explain that your point is not the *whole* story...

Look, life on Earth, like just about everything else in the real world (e.g. chemistry, physics, etc.), is not driven by any *one* force or natural law.

Instead, it is driven by multiple factors, many of which oppose each other, and the actual end results are found at the point where the various factors reach a balance, known technically as "equilibrium".

For example, thermodynamics tends to push air molecules *away* from Earth, gravity tends to redirect them *towards* the Earth, and as a result an equilibrium is reached in which we have a permanent atmosphere about a hundred miles deep, of the type we're used to, instead of an airless world from which all the atmosphere has long ago flown off into space, or one in which all the air molecules are heaped together into a thin film over the ground like a coat of wet paint, with pure vacuum above it.

Similarly, you're trying to analyze the "genome dynamics" of junk DNA by considering *only* the (weak) evolutionary pressure which would (left to itself with *no* other factors) tend in the long run to clean out the junk DNA, without acknowledging or appreciating the *MANY* other factors which would (by themselves) tend to *increase* or *maintain* junk DNA.

You can't get the right answer if you over simplify the problem.

The *actual* end result is an equilibrium condition whereby the factors tending to decrease junk DNA balance the factors tending to increase it, which is obviously going to be somewhere in "the middle" -- neither a pristinely "clean" DNA, nor one completely overwhelmed with garbage. And even just off the top of my head, 90% "noise" and 10% "signal" sounds like it's in the ballpark of a realistic equilibrium point under most conditions.

It's helpful to try to boil a problem down to its essentials, certainly, but not to the point of cartoonish oversimplification, which is what you're attempting to do on this issue. The metabolic "cost" of carrying junk DNA around is not only small, it's *NOT* the only factor at work here, nor even close to the most significant.

[Ichneumon]

If Ichneumon believes I have misrepresented his statement, then he's welcome to correct me for my uppityness. ;)

LOL -- no, you've done a good job of stating it succinctly.

[AntiGuv]

Your statement only becomes true when followed by conditional: "Natural Selection *should* favor those without the unused code, if..."

Your statement is not true as an absolute statement. It is false.

[Southack]

"Similarly, you're trying to analyze the "genome dynamics" of junk DNA by considering *only* the (weak) evolutionary pressure which would (left to itself with *no* other factors) tend in the long run to clean out the junk DNA, without acknowledging or appreciating the *MANY* other factors which would (by themselves) tend to *increase* or *maintain* junk DNA. You can't get the right answer if you over simplify the problem."

To be fair, I'm doing more than just looking at the slight pressure to clean out junk DNA; I'm also asking if we should see a predictable accumulation of junk DNA, even moreso for older species, if Evolutionary Theory is in play here.

[Southack]

"Your statement only becomes true when followed by conditional: "Natural Selection *should* favor those without the unused code, if..." Your statement is not true as an absolute statement. It is false."

I used the conditional; ergo, *my* statement, not your re-wording or re-casting, holds true.