I love science!

Especially, I love various explanations that science offers of things. I realized this the day I first read about the electron transport chain (or ETC), or oxidative phosphorylation. That’s a mouthful, but the basic principals are simple as 2+2=4.

If you want to know already, the ETC is an fairly complex series of reactions which take place in the inner membrane of organelles (thingies inside cells) called mitochondria. Among other things, what these reactions do is pump positively-charged protons across the membrane to set up an electric potential — a battery! And when the battery is sufficiently charged, it discharges to power a kind of mill. Unlike a mill which is driven by water to power a device for grinding up grain, this mill is driven by the electric potential to power a machine which puts things together – phosphate and something called ADP (the “D” is for “di”, meaning two, in this case, phosphates) – into a similar thing with three phosphates and called ATP (where the “T” is for “tri”, of course). And ATP is a miniature battery1 in itself which can be shuttled around and used to power other processes, such as contraction of muscles. Simple, n’est-ce pas?

The discovery – at least, I saw it that way personally – was for me a moment of illumination and surprise and even jubilation. It was so simple, so practical. And it’s all physics! Well, almost.

(I will admit here that I started my career as a physicist and have always loved that subject. But a lot has happened since I left the field in 1972!)

There have been other such “eureka” moments in my science reading:

  • the gorgeous, lacy filament structure of the distribution of galaxies on an unimaginably large scale;
  • the regulation of protein expression by transcription factors – in plain English, how a cell’s environment tells it which DNA recipes to use to make proteins, so a heart does not manufacture liver proteins, for instance;
  • the fact that what we see out there – cats and beautiful landscapes and cabbages – ain’t what is really there, as well as the way our brain constructs that impression (or illusion?);
  • the mechanism of plate tectonics and the movement of the plates around the Earth since their formation, including the formation at least once of one single giant continent, Pangea;
  • the way stars are formed and maintain themselves as an equilibrium (balance) between outward pressure from the “burning” interior and the inward gravitational pull of the huge amount of matter composing the star;
  • the sodium-potassium pump, a thingy in the membrane of cells, which pumps sodium ions out from and potassium ions into the cell in differing numbers so as to set up another electric potential across the cell wall, and how this can lead to a burst of electricity (an “action potential”) which can travel down a neuron and initiate the release of chemical substances which tell another neuron to do the same thing, and so on in series until a circuit sends a message to, say, a muscle or maybe commits something to memory (and whatever that may mean is also fascinating);
  • the ingenious way retinal cells massage light signals to limit traffic over the optic nerves;
  • and lots more.

I also love the way science works. What with peer-reviewing and repeating of key experiments, we can be pretty damn sure about what we have learned. Even if another theory one day supplants the current one in some field, it will have to start by explaining the same things the current one does, so we really will not have lost anything – except some ignorance.

And the things science is not yet sure of could fill books, things like:

  • how to make the physics of the infinitesimally small (quantum mechanics) cohabit with the physics of almost-infinitely big (general relativity);
  • the possible existence of other factors influencing evolution aside from the four classics – natural selection, mutation, genetic drift and gene flow;
  • just how old life is on Earth, currently thought to be around 3.5 billion
    years, but maybe more; and how did it start;
  • and much more.

In order to share my enthusiasm, as well as to provide myself with an aide-mémoire, I have put together this site which will discuss and hopefully illuminate all the above subjects and others. Granted, it’s pickings of what I find most interesting, but I hope you will too.

So let’s get started. There is some more bla-bla here or you can go straight to the table of contents or to the first page of science.

Hello universe!

Should “universe” be singular or plural? Maybe there is a multiverse and our universe is just one of its constituent parts. That subject is at the bleeding edge of cosmological physics and can’t be answered right now — may never be — but some prominent cosmologists think it might be true.

It is natural for us to wonder about what the stuff around us is. In fact, we should wonder about it. Is the world we see really composed of four-dimensional space-time, with the space part curved and expanding and maybe infinite; of particles scattered sparsely about; of fields of energy? And where did it all come from; how did the Earth get to be this incredibly beautiful place we live in (and are doing our best to destroy) and how did the astonishingly diverse forms of life come to be? How do we perceive all this and comprehend it — and what “perceive”, anyway?

Why should we care? Well, our lives depend more every day on science. Technological gadgetry abounds in our pockets and even under our skin. We may well be at risk from the way we are (not) dealing with climate change, genetically-modified foods and other substances, pollution, nanotechnology, energy sources and all sorts of other things. We should be discussing these issues and deciding about them together. But that requires knowing about these topics. So we are allowing those who make money off them to decide for us.[ref]We will avoid political discussions from here on.[/ref] In order even to begin to understand these things and take appropriate measures for the preservation and improvement of our lives and those of coming generations, we need to know something about science and what these things represent for us.

All that (yup!) is the point of this site– to get ready to assess these subjects for ourselves. In order to get through it all, we will firmly and resolutely stick to the point of view that our best — and most certainly only — means of learning about the universe(s) is through science, by which we mean a specific method developed to help us apprehend “reality” without kidding ourselves. That method is based on incessant questioning and constant testing.

For millenia, men have devised superstitious explanations of things. One far-out one tells how the Hindu god Vishnu was asleep on his coiled-up snake Ananta on the calm cosmic waters, when a lotus plant sprouted from his navel.

Vishnu napping on the serpent Ananta

Vishnu napping on the serpent Ananta. Note the lotus stem and Brahma[ref]Carving on a rock along the Tungabhadra River in Hampi, Karnataka, India. Photo by author.[/ref].

When the lotus flower opened, the god Brahma was revealed sitting on it. Brahma created male and female by splitting off parts of himself. In this way, he went on to create all living things, restoring himself after each split. When Brahma went to sleep at night, everything was destroyed, but Brahma recreated it anew the next morning. Since a day of Brahma’s time is billions of years of human time, no one notices. But even Brahma lived out his life and then the god Shiva Nataraja, the King of the Dance, performed his cosmic dance and everything was completely destroyed.

Shiva Nataraja

Shiva Nataraja doing his dance of destruction in front of a kitsch cosmic backdrop[ref]Statue in the Government Museum, Chennai, India. Photo by author.[/ref].

Until Vishnu yawned and stretched and another lotus started to grow out of his navel…

Isn’t that great? But that will be the only such story.

So what does science have to say about the world we live in and about us ourselves?

Many popular books talk about the history of science and scientists, even though their titles may suggest differently. As interesting as such topics may be, it seems to me it ought to be possible to grasp the basic scientific world-view without plowing through all those false starts and errors, tests and experiments, names and dates. Why not simply present current scientific notions without going into the gritty details of why and how we have come to accept them as valid? A simple description. Afterwards, there are lots of books for those who want to know more. (See bibliography.)

That is what we propose to do: Take a look at what we are, where we are and how it works, and all that from the point of view of science. We will try to make it simple and will not go into the math, although one or two formulas may pop up. You will certainly recognize one of them — you might even have it on a T-shirt.

But now we are already into the material of the introductory chapter, so let’s go there.

P.S. There is one more thing. In a month (August 2015), I will have been retired for ten years. Maybe this will convince me (if no one else) that I have been doing something all this time. And a project like this one can go on forever, though I am unlikely to do so myself. Entropy will get me in the end too. (If you don’t understand that, read the little essay on Entropy.)

P.P.S. Actually, the title I wanted for this site was “The universe and I”[ref]As in the name of an old movie, “The egg and I”, or a very interesting anthropology book called “The headman and I”.[/ref], but that was taken. I tried several others — to no avail. The maddening  part was that when I visited the sites with the beautiful name I had thought of, most had not been touched for years. So there is a fair amount of garbage collection to be done by the wordpress.com folks…So I settled for the french version, “L’univers et moi”, except that in french you use the objective “moi”  (“me”) rather than the subjective “je” (“I”). I don’t know, maybe I should have called it “The universe and me”…

The past

Here is the history part, without any promises of brevity. It goes from the beginning — at least as far back as we can go with any degree of certainty — to the present day.

So it starts with what cosmology and astronomy tell us.

Then we jump from interstellar space to the earth for what geology tells us.

And then the history of life as revealed by fossils, finding out what paleontology and evolution tell us.

And now we are in the present.


What atomic physics and chemistry tell us

I am, reluctantly, a self-confessed carbon chauvinist. Carbon is abundant in the Cosmos. It makes marvelously complex molecules, good for life. I am also a water chauvinist. Water makes an ideal solvent system for organic chemistry to work in and stays liquid over a wide range of temperatures. But sometimes I wonder. Could my fondness for materials have something to do with the fact that I am made chiefly of them?

– Carl Sagan, Cosmos

The early stages of the universe and the lives of stars are the matter of physics and astronomy and their offspring, astrophysics and cosmology. By the time the first living things showed up on Earth, processes were occurring which require our knowing about the phenomena described by the science of chemistry. QM is the basis of atomic physics and that is the basis of chemistry, so we are ready for it.

To do even begin a comprehensive survey of chemistry is well beyond the scope of this document. We will illustrate its usefulness and some of its fruits by considering two subjects of great importance not only to Carl Sagan but to all of us – carbon and water.

In order to do that, it is necessary to know about several sujects:

Then we move on to consider, first, the past, starting almost 14 Gya.

Science comes marching in — basic theories


Four theories of science are essential to our understanding of what our “environment” is and how it and we got that way. These are theories in the scientific sense, bodies of accepted knowledge – not at all the same thing as hypotheses. All have been tested by innumerable experiments which have found them to be true to nature. This does not mean that they will never be improved upon, but whatever other theory or extension does so must also explain why they are true in current applications.

We generally consider physics to be the most “basic” of sciences, because it is self-contained and explained by no other science. It in turn explains chemistry – and therefore geology – and parts of biology. Thermodynamics, quantum mechanics and relativity lie within the domain of physics. They are explained here, because they are necessary to an understanding of the first subject, cosmology. Evolution through natural selection is also explained here. Plate tectonics fits well into the chapter on geology. Chemistry is a fairly vast subject, more than a theory, and will be discussed with physics and also with biology.

The result of it all is that we live in a world where matter sometimes behaves like a particle and sometimes like a wave and where on the atomic scale only probabilities can be calculated. All this is taking place in a curved four-dimensional space-time in which space is expanding at an accelerating rate! And this space is not an empty vacuum, it is something. Got that? If not, you might want to read it again. But above all, do not give up. It takes some getting used to, that’s all.

And that is not all. Since mutation is random, both evolution and quantum mechanics inject the theme of randomness into our understanding of the workings of the universe.[ref]In spite of this, some scientists think the laws of nature are deterministic. I will not discuss this subject, as it tends to make my mind seize up. [/ref] Relativity brings in the vastness of the universe and the puniness of man’s place therein.

It is clear that the universe was not created for us. A much better proposition could be defended that it was made for bacteria, which greatly outnumber us and are essential for our lives. In fact, the universe was not created for us or for bacteria or for any other creature. We get along, anyway.

The bottom line is that the real, physical world is not at all as we imagine it. We really should not be surprised at this.

Now that you have the basic stuff down pat, you can go on to read about what atomic physics and chemistry tell us.

The natural universe

The chapters are arranged in some introduction and three parts.

Introduction — what this is all about

Part I — the past

Part II — the present

Part III — the future (the shortest part)

  • What happens next … and last


How scientists view the universe, and you should too

NASA's Blue Marble, western hemisphere

NASA’s Blue Marble, western hemisphere, NASA via Wikimedia Commons

In order to understand the what and the where, we start with the wherefrom and work our way up to the “Pale Blue Dot”[ref]A photograph of Earth taken by Voyager I from a record distance of about 6 billion km inspired Carl Sagan to use this term. See it on Youtube.[/ref] we call Earth. We will go through ideas from the following subjects:

  • cosmology and astronomy – the formation of matter; the birth, life and death of stars, and the subsequent formation of other stars and of solar systems and planets;
  • geology – the evolution of the Earth itself, its surface and atmosphere, what is below the surface and beyond the atmosphere, climate and the evolution of fauna and flora;
  • biology and molecular biology, paleontology – the study of life and its development, to learn about the evolution of living organisms, including man;
  • physiology – the study of cells and organs and organisms;
  • neuroscience – the nervous system and the body’s control center, the brain.

Our path will go by way of certain landmarks, theories without which we would never find our way to the understanding which we have today: quantum mechanics, relativity, plate tectonics and evolution through natural selection. And we will follow the thread of energy and how it is transformed and used.

There will be few, if any, explanations of how we came to “know” it, nor detailed analysis of the gaps in our knowledge, although some of these will be mentioned in order to keep things “fair and balanced”. Names of scientists will be avoided. We will just look at the prevalent current world-view of science as understood by this writer. As such, it is certain to be somewhat out-of-date and subject to change – and maybe soon.

Obviously, all errors or oversights are the complete responsibility of the author.

But now you are tired of promises of what we will do. So let’s get about it! Don’t be afraid, go on to read about basic theories of modern science.


John started out his career as a physicist (particle physics, for five years — remember bubble chambers?), thinking he would make a better living that way than with his other main interest, music. But doing physics is not nearly as exciting as reading about it. And then there was the job situation at the time (early 1970s). So after five years, he switched to l’informatique (IT, system programmer, etc.) with the French Centre National de Recherche Scientifique. Since retirement in 2005, he has spent most of his time reading, traveling, eating and drinking well, and being with his cats (two now) and dog and Siv.

John has often observed that when men (and perhaps women too) get older — reaching what is sometimes called the third age — their interests often change. Some become interested in world religions, one he has heard of went throught the writings of the great philosophers, some may decide to read all of Shakespeare or some other Great Author, some become engaged in a particular field or form of politics, and so on. Some of these are really great ideas and some are quite silly and that does not really matter, does it?.

John has become fascinated by things he has been reading about science, especially physics and cosmology, neuroscience and evolutionary biology. He would like to have some at-least approximate notion of current ideas of the relation between the “real” world of physics (and geology and …) and our internal mental model of it (including of ourselves). Whatever winds up on this site is the result of his attempts to structure or order his reading and his thoughts on these subjects.

He is also astonished at the lack of scientific knowledge of much of the general public. So he would also like to do a survey of how science sees things.

Like lots of people, he is occasionally seized by the need to assemble his thoughts by writing them down. Or, he may just feel like discussing something that no one available is much interested in. John does not really expect anyone else to read this. Well, maybe Siv. Sometimes. Hopefully, he will have fun anyway.

Which does not really matter in the long run… because you all know what Keynes said about that.[ref]If not, then do a search it.[/ref]

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"L'univers et moi/The universe and I" by John O'Neall is licensed under a Creative Commons Attribution 4.0 International License.