Genuine Puzzles In Biology?

Gods, there's millions of them. Although I suppose the majority are exceedingly obscure. A few of the large scale questions I would pose are:Why do we have such exceedingly capable brains?
How does consciousness work, and why did it evolve?
Why haven't plants closed the green gap?
Why hasn't a version of Rubisco without the oxidase activity evolved?
What, exactly, is the evolutionary relationship of viruses to the rest of life and to each other?
What is the nature of the link between Archaea and Eukarya?
Why do Archaea have such different membrane lipids to the other two domains of life?
How significant has horizontal gene transfer been in the evolution of higher organisms? Especially in the light of the evidence that the mammalian placenta relies on a gene jobbed from a retrovirus.
How did life get started anyway?

I'm no virologist.But as I understand it's a very open question. It's been suggested that DNA actually evolved in viruses and all living things get their DNA from a viral ancestor*. That's not widely accepted but it is widely acknowledged that many viral genes/proteins, including those that perform roles that exist in cellular life, are unrelated to those in cellular life. That suggests that the older theory that viruses are escaped bits of genome from cellular life likely to be untrue.Whatever the case they are very ancient, because viruses from the same family infect all three domains of life, but cross-infection is highly unlikely because differences in gene regulation mechanisms and sequences mean a bacterial virus cannot infect a eukaryote and vice-versa, and the same for the Archaea.* - Zimmer, C. (2006) ‘Did DNA come from viruses?’, Science, vol. 312, pp. 870—2.

Practically all variegated plants are artificially bred and can only survive because they're protected by their human keepers. There is a little chlorophyll in them which is why they can survive but they grow slowly compared to their non-deformed relatives.

RuBisCO, or ribulose-1,5-bisphosphate carboxylase oxygenase to give it it's full name, is the most common protein in the world. It's a key part of the photosynthetic process in every plant, algae, and cyanobacterium in the world.But it has a curious defect, as well the carboxylase activity which allows it to transfer carbon from carbon dioxide to sugars and starches* it also performs the reverse process, releasing carbon dioxide from valuable compounds without producing any usable energy for the organism. Roughly 20-25% of all carbon captured in plants by photosynthesis is lost in this way (which is referred to as the C2 cycle).RuBisCO behaves more efficiently under certain conditions, which is what is behind the C4 cycle of some plants (notably certain grasses, including almost all domesticated varieties), but nowhere has a variant of RuBisCO without this curious inefficiency evolved nor a means to switch off it off by activating other proteins.The puzzle is why not?* - technically it transfer carbons onto intermediate compounds from which sugars and starches are synthesized.

See here for a spectrum showing incoming light intensity; there's no green gap in it. The 500-600nm range over which chlorophyll fails to absorb light is not matched in the incoming light.

Either modifications to the chlorophyll pigment or the use of additional pigments to increase the proportion of the spectrum absorbed (as some bacteria do, although even they don't completely close the green gap). The bacteriorhodopsin protein used in photosynthesis by halobacteria (actually Archaea not Bacteria) has an absorption spectrum that is pretty much the inverse of chlorophyll so we know such pigments are possible.

If this were the case, shouldn't we expect to see, for example, shorter distances between all mammals and yeast than choanoflagellates and yeasts, whereas - in fact - the distances are very similar.