Interesting to note that there is something called “epigenome” that overlays the genes. What has been demonstrated is that environmental contaminants (from food, from smoking, etc) can affect not the genes themselves, but the activation or turning off of gene sequences. This is the epigenome, the structure of active and passive gene clumps. These changes are passed along to offspring. I don’t know if this is what Phil meant, but it is a way for environmental influences to change not just the organism itself, but the inherited structure.

Maybe I (deliberately?) misread the BA, as Irishman says. But in the text, he is describing a single event (a splitting cell) after which the gene or gene map is not the same anymore for the offspring. And I think we can agree that the environment will not directly interfere there to create a more “adapted” gene.

Anyway, as I said, that’s “nitpicking” on the Bad Astrononomer’s choice of words, and I know he meant the right thing. After all, it’s one of the few sites one can encounter not only good astronomy, but good science in general…

The only elements that are gaseous at STP and are less reactive than nitrogen are the noble gasses – making them react with anything is really hard work.

Nitrogen is relatively inert at decent temperatures (which is, I believe, why nitrogen fixation is so hard), and atmospheres decay very slowly. In fact, lifetimes for biospheres on earth sized planets in habitable zones are many Gyr. (Well, duh.)

Or maybe- Oxy-Genesis??

Panspermia

> Sorry to nick-pit, but since that’s what a huge part of the site is all about (the good nit-picking, that is): environmental pressures won’t (and never did) change any gene.

I don’t think that is what Phil meant. He is mentioning the “gene map”, which is different than individual genes. Rather, it is the collective of genes that make up a given species. Selection pressures do change the gene map of the species – they change the gene frequencies and alelle frequencies manifesting.

This is not entirely correct. There is some evidence that environmental pressures can directly influence the evolution of genes by dramatically accelerating the rate of evolutionary mutation. (but don’t take that to mean there’s some “intelligence” involved!) The simplistic “steady random mutation” natural selection taught to the public is really shamefully simplistic, its a much more complex and interesting process!

To oversimplify further, a lot of current evolutionary geneticists believe there is some type of genetic control that can “open” or “accelerate” mutation in certain genes. So, if a species is undergoing dramatic environmental change or some other pressure, their survival mechanism will kick in and attempt to rapidly mutate certain genes. It’s all quite fascinating.

Sorry to nick-pit, but since that’s what a huge part of the site is all about (the good nit-picking, that is): environmental pressures won’t (and never did) change any gene. The genes change randomly(!) and then are subjected to selection, depending on environmental pressures. No environment in the world (or other worlds) will change a gene directly to adapt to it.

Of course, the environment in the wider sense may change the gene randomly due to radiation, chemicals or other mutagens. But I don’t think that’s what BA meant…

I would have to beg to differ with you on this one. Modified RNA has some amazing properties as a catalyst and the only RNA we are familiar with is the kind that is around now; we don’t know exactly when life settled into the central dogma that we see today and we don’t know what other competing chemistries lost out, or exactly why. One thing we do know is that RNA is probably the most primitive part of the modern central dogma and that DNA and Protein are both advances that probably depended on RNA first; biology primes DNA synthesis with an RNA primer and protein synthesis depends on a complex constructed largely of RNA. This is not to say that there aren’t other chemistries, it is to say that RNA is plenty flexible to be the progenitor or the most direct successor to the progenitor.

And while O2 is a wonderful way to get energy, let us not forget that in the early earth natural radioactivity would have been MUCH MORE PRONOUNCED than what we see today. Just work back from half-lives and current abundances. Ions and gamma rays galore.

I kind of doubt these sources of energy that you are suggesting are accessible ones. First, radioactivity is a difficult thing to predict on a level where life depends on relatively reproducible interactions of one or two molecules; radioactivity is entirely stochastic and must be viewed from bulk–a single atom of an isotope with a thousand year half life will decay once in a thousand years and you can’t predict the direction the decay products will travel; that’s too slow for life and difficult to reproduce. Chemical reactions depend on molecular orientations, physical symmetries and charges, which occur reproducibly, which is why life currently uses them (including oxygen as a charge acceptor). Second, gamma rays are not generally something you want around anything anabolic; the energy of one gamma-ray photon absorption is much higher than covalent atom-atom bonding energies and such photons will destroy molecules they interact with. Visible sunlight is much better than gamma-rays as an energy source because there is much more of it and it doesn’t destroy the molecules it hits… which is why life uses it so much. Also, ions are as available today as they were back then; salt forms ions when dissolved in water (should I mention that RNA, DNA and Protein are all ions?).

If you are suggesting that RNA is too fragile to survive some protobiotic world, I would again beg to differ. RNAs can survive all kinds of organic mixtures. I know first hand of synthetic RNAs (made in organic solvents) that facilitate chemical reactions in organic mixtures. Further, volatility is not really an issue if your replacement rate is as high as your loss rate and if there is enough lag between replacement and loss for the biological function to occur and to facilitate replacement. Organometallics involving metal atoms and RNA based scaffoldings are extremely powerful catalysts.

The structure of the genetic code, the fourfold biopolymer system, and the monomers used to control those polymers all point to some sort of syncopated dance (cyclic reactions) where each did something for the others.

This statement is confusing to me. The mono-phosphates nucleotides are all identical except for their nitrogenous bases. The nitrogenous bases don’t carry out a whole lot of chemistry (if any) and the identical parts all react indistinguishably. The nitrogenous bases function largely to form hydrogen bonds and do so specifically, but in context of larger chemical structures (DNA and RNA). Four-fold symmetry only occurs in DNA and it is really just a two fold symmetry since you have Adenine hydrogen bonding Thymine and Guanine to Cytosine. This does not account for other important nucleotide bases like Inosine or Uracil (which I guess makes it a greater than six fold symmetry), or the fact that RNA and DNA would be required to have different four-fold symmetries since they don’t share the same bases. Triphosphates nucleotides are good for forming pyrophosphate, mono-phosphate or being modified into a cyclic form and these purposes are in the context of higher levels of biochemistry. Aside for spontaneously decaying as a triphosphate, I don’t think they, themselves, have any unique chemistry that another nucleotide or analog doesn’t fill and they most certainly do not synthesize one another. One of their greatest chemical strengths is to be polymerized and they become DNA or RNA or some hybrid at that point. The genetic code is actually quite degenerate and really probably isn’t the starting place of life, even though it is a marvelous mechanism that life currently uses.

I am not suggesting any abiogenesis here, but I think it is important to contribute the facts.

Actually, I was watching a show on the History Channel called something like “How the Earth Was Made”, and they discussed how the oxygen in the atmosphere caused the iron in the oceans to rust out and settle to the bottom, and that these sediments are detectable all over the globe. (Or something like that.)

While it is romantic to think that there was a point where life suddenly… BANG… changed, I think that what probably happened with a bit less abrupt.

It may well have been a case of active-site flexibility in whatever catalyst was responsible for this reaction at that time, whether RNA or Protein (or whatever predecessor). I’ve seen one modern example of a protease, which has protease activity, having its active site co-opted to the purpose of bio-condensation of silica. It is a much more evolutionarily sound model to envision a gradually evolving catalyst promiscuously using a variety of available electron acceptors and through steady, normal natural-selection pressures, eventually arriving at something that specifically prefers oxygen. This would spread the evolution over the entire population around at the time rather than specifying it to one particular chance “daughter cell.” Indeed, this mechanism fits in well with what Nigel said too. Also, there are plenty of compounds that oxidize as well as oxygen, it may well be that oxygen won out simply by volume of availability and thermodynamic free-energy preference.

And people wonder why I consider the production of, well, the entire phenomenonological universe out of the most basic laws describing the interaction of fundamental particles to fundamental forces on the small scale and the interaction of mass and energy over large distances on the large scale through emergent processes inherently spiritual.

The devil may be in the detail, but God’s in the gap between the value of the whole and the sum of its parts. That synergy’s the closest thing I have to a proper religious belief.

“. . . And somewhere, deep in all that murk, a little tiny cell split in half, and the copy wasn’t perfect. Did a cosmic ray zap it? Was there some environmental pressure that altered the gene map? However it happened, the daughter cell’s chemistry zigged instead of zagged, and it was able to use oxygen, which was probably a poison to life up until then. . .”

It is thought that oxygen metabolism initially began, not to *use* oxygen, but to detoxify it (analogous to the way Cytochromes P450 in our livers detoxify drug molecules). Then, once this detoxification reaction was occurring in many organisms (and, in and of itself, the ability to detoxify one’s environment is a significant advantage), it was only a small step to coupling the detox of oxygen to some other reactions, and thence using oxygen metabolism as a source of energy.

Good response. Never thought of it like that.

Presumably someone has measured its “blueness” at some stage using spectroscopy or some such.

I wonder if there is any liquid that is truly colourless in its pure form.

Sorry, but the sea isn’t blue. It’s colourless – it only looks blue because it reflects the colour of the sky (which is why the sea around Britain is a permanently greyish colour).

I seem to recall that the blue colour of the sky being due to the scattering of the sun’s rays by nitrogen (I’m going from memory here – could have that last bit wrong). The question I wonder is, did the young earth’s atmosphere contain as much nitrogen as it does today? If so, and if my memory of light scattering is correct, would the sea have appeared blue to any fortunate time-traveller who happened to be around 2.5(ish) billion years ago?

This is a section from a 3000+ word assignment I did last year for BioSci 210: Evolutionary concepts and events. I got an A+ (90%).

Oxidation of the Atmosphere:
About 2.3 billion years ago, once life had truly gotten under way it began to proliferate, the seas were full of photosynthetic cyanobacteria, rapidly converting the water (H2O) and carbon dioxide (CO2) that were so abundant, into CH2O (and other complex forms of organic matter) and O2 (Kasting and Siefert 2002). It is because cyanobacteria can live both anaerobically and aerobically they are believed to be responsible for the initial rapid rise of atmospheric O2 (Kasting and Siefert 2002) and studies into the cyanobacterias ribosomal RNA and portions of DNA inside eukaryote chloroplasts implies that all eukaryotes derived their photosynthetic capabilities from cyanobacteria through endosymbiosis (Kasting and Siefert 2002). This increase in oxygen levels forced a change in some of the organisms at the time. The rapidly growing amount of oxygen was building up and would eventually make it impossible to survive, but this left a huge niche for any form of life that could harness use of this oxygen element. Some microbes broke free and either modified parts of their metabolic machinery or formed symbiotic associations that permitted them to join the oxidation of organic matter to the reduction of O2 back to water (Falkowski 2006). This sky rocketed the yield from the respiratory pathway per molecule of glucose oxidized than any of the previous anaerobic pathways (Falkowski 2006). Filling this niche allowed for a new huge branch in evolution to come along and that is why this can be considered one of the most major transitions/events in evolution.

I apologize for it’s length, but editing it made it sound just weird.
Does that clarify anything? I wrote this nearly a year ago so some facts etc may be now understood differently.
(I’m so excited! my first post here where I know the subject matter!
Great boost to the ol’ ego)

Today, these unicellular lifeforms are known as politicians, although all they metabolize these days is hot air.

This is mostly true, except oxygen per se is
not a fuel. Pure oxygen is not flammable.

Then later that summer Vick & I were at the Smithsonian in DC where they had a display of stromatolites and other early life forms (eidacarians and such, really cool!). There was a timeline on the wall from the creation of the earth from planetesimals to today, and I took my green laser and pointed out to Vick where 1.9 billion years ago was. I told her “Here, Vick, here is where we looked back to that night. There was no soil on the surface of the Earth then, just rocks, gravel, lava & sand. The atmosphere was unbreathable too.” I might have been a little off on the atmosphere bit, but not by much.

It still blows my mind that I looked back to that era with my 10″ scope. Those photons of light had been travelling for all that time untill they hit our retinas. Of course, they’re falling to the ground all around us all the time, even in the day, but that night we were actually watching for them.
Rich