MortalWombat

This "irreducible complexity" thing to me is a red herring. No one marvels at the fact that if a keystone is removed from an arch, the thing will not stand, and conclude that it couldn't have been built by piling stones on one another. This is because we know that arches were built using scaffolding, and when the arch is finished, the scaffolding, now unneeded, is removed. In a similar manner, gene duplications often lead to a redundancy in a biochemical pathway, leaving one of the copies of the duplicated gene to be free to evolve into another function. If the old pathway is no longer needed by the organism for whatever reason, those original genes are lost, and it looks like this new pathway is "irreducibly complex" because you can't take away any of its components anymore.

theyeti

Yes, there is evidence that yeast (or at least Saccharomyces) have undergone whole genome duplication. See for example <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=113777 78&dopt=Abstract" target="_blank">Origin of the duplicated regions in the yeast genomes.</a>, Trends Genet 2001 Jun;17(6):302-3, and <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=953975 7&dopt=Abstract" target="_blank">Extent of genomic rearrangement after genome duplication in yeast.</a>, Proc Natl Acad Sci U S A 1998 Apr 14;95(8):4447-52. There are many other examples too. Whole genome duplications are pretty well "proven" in zebra fish (and a separate one in an earlier teleost ancestor), Arabidopsis, and Rana. It is also hypothesized that all vertebrates are octoploids, having had two complete rounds of whole genome duplication in the common ancestor. However, this hypothesis is controversial, and the amount of time elapsed and the resulting noise may mean that it can never be resolved.

I should hasten to add that even if gene duplication simply copies preexisting information, it provides a very fertile substrate for the evolution of novel genes. The fact that genes are arrayed in a relatively small number of families and superfamilies (whose members can sometimes have quite dissimilar functions though they are structurally simliar) supports the notion that most genes arise through evolution from duplicates. In fact, with the known instances of whole genome duplication, like in Arabidopsis, 70% of the duplicates have been maintained without silencing.

theyeti

[ March 16, 2002: Message edited by: theyeti ]</p>

DNAunion

DNAunion: Cooption.

NOTE: I am trying to avoid a discussion on Behe's IC.

DNAunion

DNAunion: Thanks for the links. Some of your matieral rang a bell: I remember now having heard about inferred complete genome duplications.

DNAunion: Yes, but I wasn't talking about mere gene duplications, but about additional chromosomes or sets of chromosomes.

I don't doubt that it is possible for a human (or other organism) to have a gene get duplicated without its causing serious negative affects.

But in humans, all deviations from having the standard 2 copies of all autosomes (and about the same can be said for the sex chromosomes) are deleterious at best, fatal at the worst. There are no human chromosomes that are good to have an extra copy of, or to be short one copy of (aneuploidy): nor is it good to have an additional full haploid set of chromosomes, or to be short a full haploid set of chromosomes (euploidy).

[ March 16, 2002: Message edited by: DNAunion ]</p>

DNAunion

DNAunion: If eukaryotes evolved from prokaryotes, and prokaryotes don't have tubulin or cytoskeletons, then where would the preexisting tubulin for the mitotic spindle have come from? Wouldn't the first eukaryotes have needed a mitotic spindle?

DNAunion

DNAunion: I just found another source on the origin of mitosis - it was sitting on my bookshelf.

The book "The Origins of Life: From the Birth of Life to the Origin of Language", by John Maynard Smith and Eors Szathmary (Oxford University Press, 1999), has a whole chapter entitled "The Origin of Eukaryotic Cells", of which 6 pages deal with a subsection "The origin of mitosis". But I don't see anything really good in there (if anyone else has access to the book, perhaps they could read those 6 pages and point out the good stuff I am missing).

About the only thing I got out of that material was:

DNAunion: That is, the centrosome of eukaryotes may have evolved from the attachment site of the origin of replication to the cell wall in prokaryotes; and the centromere may have evolved from the other attachement site to the cell wall in prokaryotes - that of the terminus (the point where DNA replication is complete). That suggests to me that the same proteins - or similar ones - specific to the centromere region (the protine disc called the kinetochore, where attachment of spindle fibers actually occurs) and the centrosome should be found in prokaryotes (functioning to anchor the origin and the terminus to the cell wall). Anyone know if this is so?

Nic Tamzek

Hey DNAunion et al.,

Looks like there's a bit of flow from ARN across the net, eh? My 2 cents on that ...oh, wait, I'll just put it over there.

Briefly on the origin of eukaryotes (& mitosis etc.). The basic theory, advocated since the '70's, has been that phagocytosis (eating bacteria by absorbing them, or perhaps very initially just by sticking to them, then sticking & forming a pocket, etc.) was the key innovation from which everything else followed, mitosis included, symbiosis (symbiosis is easiest to imagine with critters that can eat bacteria), sex, cilia, etc. followed.

The guy who has worked all this out in the most detail, and published innumerable articles (almost; dozens and dozens, and they are usually very long) on this topic is Tom Cavalier-Smith.

E.g. go to pubmed for a very incomplete list (type 'Cavalier-Smith'):

<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=&DB=PubMed" target="_blank">http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=&DB=PubMed</a>

...searching the <a href="http://www.webofscience.com" target="_blank">web of science</a> on 'cavalier-smith' brings up only 22 references, but searching 'cavaliersmith' run together brings up 79 older ones.

E.g., he pretty much started with this:

ORIGIN OF NUCLEI AND OF EUKARYOTIC CELLS
CAVALIERSMITH T
NATURE
256 (5517): 463-468 1975

Document type: Review Language: English Cited References: 53 Times Cited: 100


And just last week, coincidentally, this article came out which updates his thinking in a thorough way, although annoyingly the article so depends upon an understanding of his previous work that it is hard to recommend it to beginners:

<a href="http://ijs.sgmjournals.org/cgi/content/abstract/52/2/297" target="_blank">http://ijs.sgmjournals.org/cgi/content/abstract/52/2/297</a>

...check out this abstract, it's almost as long as some articles...

There are numerous points on which TCS takes a controversial stand in this most recent paper, discussion would take too long but MHO is that he's more right than not. One big advantage TCS has is that he's been around since long before the DNA sequencing stuff came in, and so he actually has a deep understanding of microbial morphology (he's actually looked at them under the microscope/electron microscope), and so he can do far more than just stick sequences in a computer and propose a nonsensical theory for early evolution based on the results, which frankly is how a lot of other theories (eukaryotes-first, etc.) came about.

E.g.: long-branch attraction is a key issue, particularly for organisms that have passed through a hyperthermophilic stage, like euks and the ancestors of archaebacteria. Because this kind of thing results in more rapid evolution, the long branches as seen on esp. the rRNA trees are probably artefacts. Kiss Woese goodbye, archaebacteria and eukaryotes originated late (very late if you believe TCS on the fossil record, I'm not sure one has to...) and are sister groups.

If the previous paragraph made no sense, sorry, I've gotta go get pizza.


Anyhow, the articles TCS self-cites in the 2002 paper, they are the crucial ones to read before the 2002 paper although I have only read about half of them. A bunch of them were published in 1987, that work is the foundation for the 2002 stuff. E.g.:


There's one on the cytoskeleton too which is good also but I don't have the ref handy.

In other words, if you're wondering some early event in evolution, check Cavalier-Smith as he's almost certainly already published a long paper on the topic.

Regarding conservation & homologies that DNAunion mentioned, the important thing to look at is homologous proteins across bacteria, archaea, and euks, particularly between the latter two. There are many of these listed in TCS's 2002 paper (and this paper also:

<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=118373 18&dopt=Abstract" target="_blank">http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=118373 18&dopt= Abstract</a>

Some important proteins with homologs in prokaryotes are:

tubulin
actin
dynein

...some of the major components of the cytoskeleton, mitosis, and cilia, notably.

OK, I gotta go before the pizza gets cold.

Later folks,

Nick


PS: The whole paragraph that Behe spends on indirect pathways in DBB is maddening -- it's just a cop-out escape hatch as far as I can tell. Fact is, indirect (but basically gradual) pathways, meaning those where the selected function changes once or multiple times, are overall the key to understanding the evolution of 'irreducibly complex' systems. Behe's whole book should have been about criticizing indirect pathways if was going to attempt to make a truly serious argument. Instead, he just plain asserts that they are improbable.


PPS: OK, I have a minute still. IMO the primary things that are limiting TCS and the rest of us in understanding the origin of eukaryotes, mitosis, etc. further are:

1) Incomplete knowledge of replication mechanisms in eubacteria (although this has improved rapidly in recent years), archaeabacteria (this is almost unknown) and in euks, particularly all of the various obscure single-celled phyla that no one except people like Cavalier-Smith study. This stuff is the very definition of obscurity. Yeast are great model organisms and all but they're pretty highly derived.

2) Deep phylogeny. Getting robust phylogenies gets tougher the further back you go, and if TCS is right then the deep branches of the rRNA tree don't really tell us much except that archaea and euks went through a phase of rapid evolution due to adaptation to high temperatures basically (this is what TCS's 'quantum evolution' means, just to head off the antievolutionists on this one). TCS argues that one must incorporate fossil evidence and fine-scale morphological evidence (e.g. cilial root patterns) as well as diverse molecular evidence (hundreds of proteins) to root and relate the trees of the three domains. Probably no one would really disagree with this fundamentally, but people have tended to get caught up in the simple rRNA paradigm and taken it as the last word which it is not.

3) Focus on parasites and diseases in microbiology. There are obvious good reasons for this, but for those interested in evolution one must remember that intestinal E. coli is perhaps not the best model for all things prokaryotic. Ditto for numerous other cases: disease-causing organisms may be well-studied but the data bias that results should not be ignored.

...and...

4) Similar to #3, one must remember just how unexplored the microbial world out there really is. We discovered a whole new group of archaea recently, IIRC correctly, and we still haven't been able to culture them (the whole dependency on culturing results in another big bias in our data -- until recently, if you couldn't culture a microbe it was basically invisible).

5) Would be to resolve the fossil record. Euks are oft-cited to originate in the fossil record ~1.5 billion years ago, but TCS says that those aren't euks. at all but just big prokaryotes. The chemical evidence for early archaea and euks is also ambiguous according to TCS. #5 here is less important but would be nice to resolve IMO.

[ March 16, 2002: Message edited by: Nic Tamzek ]</p>

DNAunion

DNAunion: I have read in one source (though I don't know what it was) that a tubulin-like protein was detected in a prokaryote, and that although there was no true cytoskeleton, there were some "fibers" of some sort in the cytoplasm. Reading something only one time - that if it is true, should be repeated many times - makes one wonder if the finding was called into question after being published (but then again, I don't read the primary literature as much any more: I started rereading my college texts because that is the material I need to know to tutor). So, does anyone know if is it now fully accepted that there are "ancestral tubulins", shall we say, in prokaryotes? And if so, does anyone have any recent references?

Concerning actin in prokaryotes...what does it do? For example, in animal cells actin (along with myosin) forms the beltlike contractile ring responsible for the cinching action (forming the cleavage furrow) involved in cytokinesis. Does actin in prokaryotes play a similar role by "pinching the bacterium into two" during cell division?

Nic, one piece of constructive criticism. Although I appreciate all the time and effort you invested in posting all of that material, I wasted time reading all of it because little if any of it dealt with the questions I raised. The material was more on the origin of eukaryotes in general than on the origin of eukaryotic cell division specifically (few or no mentions of the mitotic spindle, kinetochores, cyclins, cdk's, etc.): phagocytosis and endosymbiosis may be interesting, but they aren't mitosis.

[ March 16, 2002: Message edited by: DNAunion ]</p>

Nic Tamzek

Look up 'ftsZ' and 'tubulin' on the web or pubmed, you'll get lots of stuff. It's as close to consensus as things get AFAICT.


TCS 2002b (March) discusses just this at some length. Do searches on 'actin prokaryote homolog' and such and you'll get the homology references.

For dynein, look up 'dynein AAA ATPase' and similar things. Mocz & Gibbons are the authors I'm thinking of.

But, phagocytosis is crucial to getting from prokaryote replication to eukaryote mitosis. The origin of every complex structure must be looked at in phylogenetic, functional, and organismal context, a ubiquitous ID mistake is to focus on one particular system (e.g. mitosis in an advanced eukaryote like yeast), and consider it in isolation. The only way to begin to get at the evolution of complex things though is to consider everything across as many organisms as possible (which is why I was complaining about the data bias in looking at disease organisms above, BTW). Which is why you should read all those Cavalier-Smith articles...

Symbiosis is a by-product of phagocytosis -- as is mitosis.

Sorry, I gotta go.

nic

PS: Look up 'pleuromitosis' for example.

DNAunion

DNAunion: I just looked up pleuromitosis on PubMed. I got 2 hits. One was in French and had no abstract. The other article is in Russian, but does at least have an English abstract. So from searching PubMed all I got was:

DNAunion: I understand that pleuormitosis is considered simpler than mitosis (and an intermediate between prokaryotic cell division and true mitosis), but what does mitosis have that pleuromitosis doesn’t have? The abstract mentions centrioles, microtubules, and an MTOC, and the book I referenced earlier by John Maynard Smith has a diagram of pleuromitosis with labels for centrosome, chromosome, centromere, and division furrow, and it shows motor MAPs (though it doesn’t label them), and the chromosomes are linear.

And what exactly is pleuromitosis? None of my college texts I read (two on cell biology, one on genetics, one on biology in general, one on zoology, and one on anatomy and physiology) don't do any more than say that it exists – including the text “Molecular Cell Biology: Fourth Edition”, which has the longest and most detailed discussion devoted to mitosis of any of them. From what I can gather from the diagram in the John Maynard Smith book, pleuromitosis is "mitotic nuclear division" that occurs in the nucleus itself, as opposed to normal mitosis in which the nuclear envelope is “dismantled” and the processes involving the chromosomes (and the structures that interact with the chromsoomes) occur in the cytoplasm.