Rip:20

How is the mosaic modular nature of enzyme evolution convergent? Also, if you read the article the changes in non-coding regions are the opposite of useless since they altered phenotype. That's the whole point of the study, that non-coding regions have important regulatory and expression effects. Evolution works across the genome on much more than just composition of protein coding regions (genes).

Hehe. They're struggling in the rocket dept. too. Fail

Well if it's biotic then you should check the autoclave setup. 250 C, high pressure, 30 minutes should get everything. Tin foil top, keep it covered. Why are you storing at 60 C. That's flippin hot! Try the fridge.

LOL. I have certainly sustained some damages to my psychological mind. Otherwise, the question of virus origin is truly fascinating because it stretches the canonical definition of life for me. Unlike cellular life, viruses (and virus-like particles) lack a set of conserved genes with which we could infer past evolutionary relationships from. Plus that virus-like behavior can be derived from DNA or RNA with or without proteins, or proteins with out nucleic acids, says to me that it is perhaps an intrinsic property of both protein and nucleic acid polymers above a certain size, and that the extant lineages of viruses (and VLPs) have multiple evolutionary origins. Think about that for a minute. This contrasts with our view of cellular life, all of which appears to have a shared common ancestor. This is legendary. +45

Yup. The stuff I see used to meet the NSF's somewhat new "broader impacts" evaluation criteria are often pretty funny post hoc add ons. A common easy cop out is that the grant will enable training opportunities for students. Not that that's not an admirable goal, but it's actually good to come out of our strange obsessions sometimes and think this stuff through. Although there might not be a directly visible route to an application, you can still use your imagination to come up with stuff that at least meshes with your hypotheses a bit more directly.

It only works if you have a pure culture of bacteria and only about 5% or so of bacterial "species" can be (have been) isolated into cultures. Furthermore, absence/presence of an outer lipopolysaccharide layer is not a monophyletic trait. (Nor is chlorophyl +/- in Euks either for that matter). So while Gram staining is a good tool for instructional microlabs, it's utility in current research science is extremely limited. But of course you can do whatever you want, which is a part of what makes science great. As of 2007 we are up to 30 phyla with cultured representatives and 70 phyla defined solely by culture independent techniques for Bacteria. (Based on 16s rRNA sequence space.) Using metagenomics and metaproteomics (among other techniques, like good old fashion culturing) we are just beginning to scratch the surface of the accompanying phenotypic/metabolic diversity. It's both an overwhelming and exciting time to be a microbiologist.

This is akin to saying there are two types of Eukaryotes: chlorophyll positive and chlorophyll negative. Although not incorrect, it's a superficial delineation based on a characteristic that's very easy to measure but provides limited biological insight. Same with gram staining, it was once an important method for describing bacteria (couple of decades ago), but has since been replaced with more descriptive measures.

Requires hours of autoclaving to destroy? How about Methanopyrus kandlari, which actually grows in an autoclave. Yup, grows in 121 C water. Native to deep sea thermal vents. My link

Intelligence, although it's a difficult term to define, is simply not a requisite for evolution to occur, as you claim in your original post. Memory (or information storage) is required for both evolution and intelligence. Since Griffith's work in the early part of the last century, we've known that strings of DNA are the information storage system for all cellular life. Most of the points you make only support evolution, rather then call it into question. The issue you bring up about oxygenic photosynthesis seeming to be in balance with aerobic respiration is just one of many successful cyclical systems life has evolved.

Exactly. ^^ Also, to the OP: cellular memory = DNA. But memory ≠ intelligence. A book is a form of memory, but you would not call it intelligence. DNA is a form of information storage, but not intelligence.

This is a great topic that is often misunderstood. I'll put my vote in with the bacteria (being a microbiologist), mainly due to the awesomeness of HGT. I want to point out that the Archaea have the shortest branch length (slowest changing), followed by bacteria, with Euks having the longest branches in the ribosomal tree of life. I would also like to say that sometimes evolution works by not changing (purifying selection).

This is awesome. Where did you come up with this? I'm requesting more details.

But sometimes evolution does select for simplicity. Think of the genome reduction in Pelagibacter ubique, or your own example of loss of unused traits in parasites (could be drift in some cases, could be positive selection to reduce waste). The point is there is no one direction or plan that evolution follows for all life forms. In terms of Eukaryotes v.s. Bacteria, yes the bacterial domain has far more metabolic diversity in total, and some members are massively versatile (i.g. large genome pseudomonads), but no one individual bacteria rivals a crown Euk (i.g. human) in terms of differential multicellularity, or even total protein diversity.

The disconnect is that not all life has followed the pattern of evolving from simpler forms into complex multi-cellular forms. So the premise of the article you site is not a generalizable principle of evolution. My counter-example was bacteria, but there are many others too. The bacterial lineage is just as old as our own Eukaryota, it's just gone a very different, but highly successful direction. Sometimes evolution selects for simplicity.