Genuine Puzzles In Biology?

Creationist nonsense apart, there are some things in nature which make you think: "Why in the world should it be like that?"The hairlessness of humans is one instance, there's been a lot of debate about that.Another thing which has long puzzled me is the conservation of cervical vertebra number in mammals. With only two-and-a-half exceptions, mammals have seven vertebrae in their necks, no matter how long or short their necks are. Now, this number varies wildly in other classes of vertebrates; and also in mammals themselves the number of other sorts of vertebrae are not fixed at all: the number of dorsal vertebra can even vary within a species. Why should the number of cervical vertebrae be so invariable?So would anyone like to add to the list? What is genuinely puzzling in biology --- what are the questions that need answers and don't yet have them?

Thread copied here from the Genuine Puzzles In Biology? thread in the Proposed New Topics forum.

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?

This question most interests me of the ones you posed, Jack. Perhaps mainly because I don't understand most of the other ones.How open is this question? By that I mean, is it clear that there is a relationship, but the exact nature is unknown? Or, is it possible that they in fact have separate origins?BTW, great topic, Dr. A!

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Ridicule is the only weapon which can be used against unintelligible propositions. Ideas must be distinct before reason can act upon them; and no man ever had a distinct idea of the trinity. It is the mere Abracadabra of the mountebanks calling themselves the priests of Jesus. -- Thomas JeffersonFor we know that our patchwork heritage is a strength, not a weakness. We are a nation of Christians and Muslims, Jews and Hindus -- and non-believers. -- Barack ObamaWe see monsters where science shows us windmills. -- PhatIt has always struck me as odd that fundies devote so much time and effort into trying to find a naturalistic explanation for their mythical flood, while looking for magical explanations for things that actually happened. -- Dr. Adequate

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.

I know it's an old one, but why are there no truly green mammals?

Thanks for participating. But could you be a bit more detailed? For example, you list: "Why haven't plants closed the green gap?" Now let me speak for 999 out of 1000 people posting here when I say that I have no idea what you're talking about.Your post would be more useful if you spent a paragraph or two explaining what the question actually is, like I did with conservation of cervical vertebrae number in mammals. I explained what I was talking about, and I explained why it was puzzling to me. Could you do the same?Thanks.

Plants don't absorb green colored light. There's a gap in the spectrum of light that plants can absorb. Why haven't they closed that gap and become capable of absorbing green light?

Because they would then have black leaves, and poets would be robbed of a huge inspiration?Yes, I think this could be a fantastic topic!

My cousin planted some of these plants with white leaves: I was all: Are they reflecting all the light? How do they live?Not that they've closed the green gap, but... yeah, whatever. They're neat.

Great topic, Dr. A.This is my biological puzzle.Most insects mate by coupling the genitalia at the terminal segments of of the abdomen.Odonate mating is much more complicated. Both sexes still have genital openings at the end of the abdomen, but the male also has accessory genitalia on the second abdominal segment.The male transfers sperm packets to the accessory genitalia prior to mating. He also has appendages at the end of the abdomen that are used to grasp the head of the female (in dragonflies) or the pro-thorax or meso-thorax of the female (in damselflies). Now these male appendages are unique to each species and can be quite intricate with lumps, depressions, spines, hairs, etc. and the fit quite specifically with the female, kind of like a lock and key, but also stimulating sensory regions.Occasionally, males of another species will attempt to mate with a female by grasping her head but she will not copulate unless she senses a male of her own species.Once the male is coupled with the female, she will swing her abdomen forward until the tip contacts the male's accessory genitalia. Here we have more intricate apparatus, that not only transfers sperm to a special organ in the female, but may also scoop out or pack down (depending on species) any sperm already there from prior matings with competing males. This copulation may be very brief (a few seconds) to many hours, again depending on species. Most species can fly around quite well in this wheel position and it may be a common sight around aquatic habitats in the Summer.The male may remain attached to the female while she oviposits or he may guard her to keep other males from mating.I have spent most of my life studying dragonflies and their mating. It is extremely complex, not just in morphology but also in behavior. There is a fairly large community of scientists who study Odonates and none of us has offered what I consider a really satisfying explanation of how their mating morphology and behavior evolved.

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What if Eleanor Roosevelt had wings? -- Monty PythonYou can't build a Time Machine without Weird Optics -- S. Valley

Sir, I salute you.

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.

I found one hypothesis to explain this, from here*. The basic idea is that, in mammals, the control genes regulating the expression of cervical vertebrae also regulate the rate at which cells reproduce. Any significant change to these runs the serious risk of making you very cancer-prone. Apparently, experimental studies on mice show that changes in the expression of certain control genes increase the expression of both cervical ribs and cancers, and there is supposedly a high correlation between the appearance of cervical ribs and childhood cancers in humans.*It's an excerpt from Glbert, S. 2006, Dev Bio, A Companion to Developmental Biology