Tuesday, 4 February 2014

Yes, I believe in molecules

In reference to an article I have recently read (http://www.fromquarkstoquasars.com/do-you-believe-in-molecules/), yes, I do believe in molecules. And this article gave me the idea for one of my own here in Science At Hand.

I still remember how difficult it was at the university an important subject during the first semester. A subject named something like “Chemical bond and structure of the matter”. It consisted in hours and hours of lessons about the atomic and molecular structures, the different chemical bonds, and things like that. But we had to learn that if we wanted to get one day the BSc in Chemistry, so there was no chance…

How could I explain a few things about the atoms, the molecules and the structures of those molecules? I don’t want to spend days talking about it, and I want to give just some clues about the topic… in a comprehensive way if possible!

So let’s start for what we know about atoms (and be assured that I will not talk about the atomic bomb!). The word atom comes from the ancient Greek (again!) and means “indivisible”. And this is the first problem we find when trying to understand them, you will see why in a minute. The term “atom” as the smallest unit forming the matter was proposed by early Indian and Greek philosophers, and it was rescued by chemists in the 18th and 19th centuries after showing that those atoms could not be broken down by chemical methods. Then, by the late 19th century and the early 20th century, physicists discovered substructures inside the atoms, but even with the word atom not being suitable anymore the name was kept. Hey, I cannot help it!

The point is, atoms are made of protons, neutrons and electrons. Each atom has a nucleus with protons and neutrons, and this nucleus is surrounded by electrons. I am pretty sure you have seen an image like this:

Keeping aside the inaccuracy of this model of the atomic structure, it fits with the concept: the atoms have a nucleus surrounded by electrons. Let’s stick to this idea, then.

All matter is made of atoms. OK, this simple sentence is well accepted by the public, which is a good thing. But when we talk about the oxygen that we need to breathe, or about the ozone layer, to put examples commonly used outside the scientific world, we are not talking about atoms, we are talking about molecules. Or when we mention the carbon dioxide which causes a greenhouse effect when accumulated in an excessive quantity in the atmosphere, carbon dioxide is a molecule. And water is probably the most important molecule for us!! (Logically, when we talk about these molecules, we refer to incredibly huge amounts of molecules of the said substance grouped together -thousands of millions of them, actually-... otherwise we would die of thirst if each time we drank water we were drinking just one molecule of water!!!).

So we should go to the next sentence which should be accepted and understood: atoms combine between themselves to form molecules. Therefore, water is H2O, a molecule formed by two atoms of hydrogen and one atom of oxygen. Looks very basic, but this simple fact allows the wonder of water, with all of its properties. Carbon dioxide is CO2, one atom of carbon and two atoms of oxygen. The oxygen we breathe, molecular oxygen, is O2, two atoms of oxygen. And ozone is O3, three atoms of oxygen.

How are the atoms able to combine with each other to form all these substances? Well, that’s where the periodic table comes into the game. Yes, that image which causes nightmares to many just when they see it! But the periodic table is a very useful tool, believe it or not. Mr. Dmitri Mendeleev did a really good job, no wonder.

(First thing for you to know: why periodic table? Well, we see the elements arranged into rows and columns. The rows are called periods, and the columns are named groups. Now we can move on.)

The atoms of each chemical element have intrinsic properties according to their individual structures. Let’s take hydrogen and have a look on the increasing complexity as we move along the periodic table:

Hydrogen is the simplest atom. It consists of a proton and one electron. Yes, you read well, only one proton and one electron. Simple, ain’t it? The atomic number -which is the number of protons in the atomic nucleus- of hydrogen, then, is 1. (Just to mention it, though I am not going to talk in detail about it, the elements have isotopes, which are the same elements but with a different number of neutrons in the nucleus, and therefore they have a different atomic weight: protons and neutrons are the components of atoms which have a weight, while electrons are weightless for they are too small, thus the atomic weight is determined by the protons and the neutrons in the nucleus. Hydrogen has three isotopes, protium -without neutrons-, deuterium -with one neutron- and tritium -with two neutrons-. The term protium is rarely used, though, as we generally assimilate hydrogen to this one isotope.)

What is the next element, in terms of complexity? Helium, of which the atomic number is 2. Its nucleus has 2 protons and one or two neutrons (there are two isotopes of helium, one with just one neutron in the nucleus and another one with two), and then it has two electrons around the nucleus. And as we go along the periodic table, the elements are arranged by increasing order of atomic number, and they are organised in periods and groups. But there is an asymmetry in this table, why? We will see it in a future article -the explanation is not short-.

Each element has specific properties that are caused by the atomic number. And more specifically by the number of electrons and how these electrons are organised around the nucleus. Let’s imagine each element as a citizen in a city, as an individual with a specific personality. There is one thing that all the elements like doing, as it was written in their DNA: they arrange the electrons in different “orbits” (actually, they are called orbitals) around the nucleus, at different levels of energy, and each of these orbits can accommodate a specific maximum number of electrons… the elements love having the most external orbit filled with the corresponding number of electrons, and this is what gives each of them its properties. Here are some examples:

-Hydrogen just needs a second electron to feel happy. With 2 electrons he feels fine, like a pair of shoes. Or if he loses the electron he had and becomes a positively charged proton, he is quite OK too. (By the way, when an element loses or wins electrons and becomes electrically charged, it becomes an ion).

-Helium already has 2 electrons so he doesn’t show much interest in the world outside. From the chemical point of view, helium is inert. When in 1903 it was discovered there was a big amount of this gas (it had been first isolated in 1895) in a mine in Kansas, they tried to burn it in vain. That's because helium is not flammable.

-And there are elements with a craving for 8 electrons on their external layer (in these cases, they follow the octet rule), and elements with high atomic number who might look for 12 or 18 electrons.

So the elements lose, share or steal electrons from their environment when necessary, in order to achieve the suitable number of electrons they need. Some elements share or exchange the electrons without too much noise, but others can be really aggressive. Any element not having the external orbit duly filled will steal, beg, arrange deals, whatever is necessary, to get the correct number of electrons. If they need 8 electrons and they have less than those 8 they look for, they will try to grab them from their neighbours or convince neighbouring elements to share electrons with them; if they need 8 electrons and they have more than those 8 electrons, they will tend to give away the extra ones.

Many times, life is beautiful and the conflicts are solved by sharing or exchanging electrons so different elements can live in harmony. When this happens, different atoms form a molecule which is a little bit like a happy family where an atom that likes giving away an electron gladly shares it with an atom that likes getting an extra electron. But then sometimes two different molecules react, as in an interchange between couples, so molecules which seemed to live in harmony decide to go for a change in their lives (the different elements are attracted by the exciting electron exchange which will generate new molecules). And this is the base of the chemical structures of molecules, and of chemical reactions.

More chemistry to follow in a future article!!

Saturday, 7 December 2013

And Then Came The Polymers

What are the polymers? Well, this is a huge family of substances, and they can be synthetic or natural.

The term “polymer” derives from the Greek words “polys” (many, much) and “meros” (part). Thus, each part, or unit, is called “monomer” (as “monos” is “one” in Greek). So a polymer is made by monomers, but, what this exactly mean? A polymer can be described as a chain formed by monomers, being each monomer a subunit that is repeated all along the chain. For example, polyethylene consists of subunits of ethylene (C2H2) repeated one after the other. It sounds quite logical, don’t you think?

Now why would I like to talk today about polymers? Because I wanted to talk about the polymers that are present in life forms. As biochemistry is the chemistry of life, these natural polymers are called biopolymers. There are three main types of biopolymers: polysaccharides, polypeptides (a.k.a. proteins) and polynucleotides.

Let’s start with the polysaccharides, then. Under this seemingly strange name we find something we are indeed quite familiar with: sugars (here I am using the general term sugars for the whole family of saccharides; when I refer to the sugar everybody knows I will use it in singular, just “sugar”). Actually, the “-saccharide” ending comes from the Greek “sacchar”, which means sugar. Another term used for polysaccharides is carbohydrates.

Glucose, a famous member of the family of sugars, is a monosaccharide. Other examples of monosaccharides are fructose and galactose. There are many different monosaccharides. What happens if two monosaccharides get chemically bound to each other? Then we get a disaccharide. Examples: sucrose, or saccharose (made of glucose and fructose) and lactose (made of galactose and glucose). So what is a polysaccharide, then? I would define it as a ramified (non-linear) chain of monosaccharides of a rather significant length. A polysaccharide may have between 200 and 2500 monosaccharides joined one after the other!

And what is their role? Well, they can have many different functions. For example, starch and glycogen are energy storage polysaccharides (glycogen means “generates glucose” so you can guess what is it made of… yes, glucose units linked together one after the other!). Polysaccharides can also be structural, like the cellulose in plants and the chitin forming the shield (exoskeleton) of some insects.

They can also have more than one function at the same time, like hyaluronic acid (a.k.a., HA). This HA, even with its “acid” name which would sound as a not nice thing, is very important. It is able to retain a lot of water molecules so it provides moisture (and remember that we humans NEED water), but it also acts as a lubricant between cells, it is an important component of the cartilage, and it is involved in skin repair, movement and proliferation of cells, and plays a role in innate immunity. It has even been suggested it plays an important role in brain development! Another example of a multi-functional polysaccharide is the beta-glucan: it activates the immune system, and it reduces the concentration of cholesterol in blood (so if in the supermarket you find “beta-glucan-rich” cookies, you know where the interest on buying them may lie).

Before I move on to the second group of biopolymers, I would like to make a point on the relevance of glucose. This is just a monosaccharide, but it is a very important one. To mention a powerful example, when we eat anything with sugar and the sucrose is converted in our body into the separate components (glucose and fructose), we are getting the only nutrient, glucose, from which the brain gets its energy… exclusively!! (Only in certain “desperate situations” does the brain use other substances to obtain energy). Of course we need a balance of how much glucose do we intake, so please be moderate about eating sweet things!

But here is a curious thing about the glucose: it is so much important, known and famous that a lot of biochemical substances related to it derive their name from “gluco-“ or “glyco-“. For example, the aforementioned beta-glucan, or proteins which incorporate polysaccharydes into their structure (yes, this happens!) that are named glycoproteins, and if they incorporate many sugar chains then they are called proteoglycans. Even the chemical bond between monosaccharides is called glycosidic bond!!

Now let’s go on with the polypeptides. Or proteins, which is a much simpler word. In this case, the subunits that form them are the amino acids. Again, we find the “acid” word on the name, and again, our cells live with it. But where does this “amino” come from? Well, you might remember the unpleasant smell of ammonia (NH3). And yes, the amino acids contain nitrogen (the amine group is –NH2). Actually, in this case the amine group has a basic character which counteracts the acidic character of the other side of each amino acid. (Please remember that an acid gives a low pH and a base gives a high pH, and that the normal physiological pH is 7.4).

As opposed to monosaccharides, for which there are many of them, there are only 20 amino acids that form the proteins. Apart from that list, there are a few more that we can find in nature, but those 20 are extremely important.

The chemical union between different amino acids is called peptidic bond, and a relatively short chain of amino acids, smaller than a true protein, is called a peptide. Where does the difference between peptide and protein lie? Well, in general a peptide can consist of up to 50 amino acids, while a protein is much larger (it is made of one or more polypeptides arranged in a biologically functional way). The order in which these amino acids are linked is the sequence, and this sequence determines not only the structure but also the function of the peptide or the protein.

Again, proteins can have many functions. If the DNA is the “instructions manual” of the cells, proteins are the “machinery” that DOES the work. And like in a manufacturing plant, the shape determines the function of the protein (if the three-dimensional structure of the protein has a mistake, it will not work properly). There are proteins meant to stay inside the cells, proteins meant to go to the cell membrane and stay there (the transmembrane proteins), and proteins meant to go outside the cell (extracellular proteins, like the collagen).

An interesting example of a transmembrane protein function is the receptor of insulin. Insulin is a peptide hormone which regulates the content of glucose in blood, as its excess would be toxic. So how does it do that? The peptide is “recognised” by a receptor, so they specifically interact like a key is able to unlock its corresponding door. This triggers a signal inside the cell to uptake glucose (by another transmembrane protein which binds glucose and then makes a kind of tunnel -called channel- so glucose ends inside the cell), and the same signal activates the storage of glucose into the polysaccharide glycogen, the glycolysis (the obtention of energy from glucose metabolism) and further storage of energy in form of fat (fatty acids).

A lot of processes in our body are regulated in such a way (with biochemical messengers being “captured” by receptors which then instruct the cells to activate this and/or deactivate that). It is just amazing that with only 20 amino acids there are so many different proteins with so many different functions, and also so many small peptides, each one capable of a specific role as a messenger for certain functions (immune system, cell division, cell movement, etc).

There are even proteins which help other proteins to achieve their correct three-dimensional structure!! And proteins in charge of destroying the proteins which are too damaged to do their job!! And all this with only 20 amino acids!!!

And then we get to the last group I mentioned before: the polynucleotides. This might be the most difficult to explain but I think it is also a very exciting group of biopolymers. First, to understand what a nucleotide is we have to imagine a molecule consisting in three parts, being the central one a monosaccharide. The two famous polynucleotides are the DNA and the RNA, and in these names the D and the R stand for the monosaccharide name: deoxyribose and ribose. DNA means “deoxyribonucleic acid”, and RNA means “ribonucleic acid”. And just to satisfy the eventual curiosity of some readers, the “nucleic” part of these names comes from the place in the cell where we normally will find them (the mRNA -we will see later what it exactly is- is, at least when referring to the RNA, sythesized there): the nucleus. Again and for the third time in this article, the “A” stands for “acid”, but polynucleotides are, as you may imagine by now, very important and our cells don’t have any problem with these “acids” running around. (Anecdotically, I can also mention that a famous vitamin, the vitamin C, is also known as ascorbic acid, and you may as well remember I mentioned earlier in this post the fatty acids, so there are plenty of examples of acids we don’t only live with but also live from).

So back to the definition of a nucleotide: we have a monosaccharide (deoxyribose, D, or ribose, R), with a nitrogenous base bound on one side and one phosphate group bound on the other end. These phosphate groups are what give DNA and RNA their “acid” character. So here we have two strange things around a sugar (here I mean the general term for saccharides). And today I don’t want to mess around with chemical structures, but as their names indicate, the phosphates contain phosphorus and the nitrogenous bases contain nitrogen. It might not be of much help now, but this is just to give an idea of what they are made of. Nevertheless, these nitrogenous bases are better known by their one-letter-nicknames: in DNA, we have A, T, C and G; and in RNA we have A, U, C and G. I know, DNA is very famous, while RNA is like the hidden brother very few have ever heard of, so A, T, C and G are letters many have seen, but what’s that U in the RNA?? I beg you a bit of patience, we will get there later…

So again, in order not to lose track: a sugar, D or R, a phosphate on one side, and one of these A, C, T, G… on the other. So how does the DNA form its well-known 3D structure? Rather easy! The phosphates bind the sugars one after the other, so we get the sequence phosphate-sugar-phosphate-sugar-phosphate-sugar-…, and the bases (A, C, T, G) get exposed to the side. And, complementarily, there is another chain going the other sense (antiparallel), doing the same arrangement. And most amazingly, each chain exposes its bases complementarily: every A matches a T and every G matches a C. And then comes the real magic: this antiparallel arrangement would look like a wooden ladder, but the nature of this structure makes it twist so it is more similar to a spiral staircase. That’s it! Voilà! Double helix formed!

The RNA gets arranged in a single chain (single-stranded), but there is a trick on the way it works so even when it is less spectacular than the DNA it is still crucial. In our DNA we have all the instructions, which means we humans have around 20000 protein-coding genes spread though the length of our genome (three billion DNA base pairs!!!).

But even when it is quite convenient to store all that information in the double helix inside the nucleus, there is not enough room so the DNA is usually coiled and condensed. Which means that, if a particular cell needs to produce a protein for a needed function, first we need machinery to identify where on Earth the coding gene is located, and unfold that section of the genome. And then, and only then, the cell machinery in charge of producing that protein will be able to start the process.

So to make things easier, from the double-stranded DNA segment, first a single-stranded RNA molecule is produced. This much smaller RNA chain (called messenger RNA, or mRNA) contains the necessary information for producing the protein so the DNA can be coiled and condensed once more in order to save space again. This process is called transcription. And here is where the T from DNA gets transcribed into an A in the RNA, but an A in the DNA becomes a U in the RNA. So the transcription consists in synthesizing the complementary mRNA chain to what’s written in the DNA sequence. Then why U instead of T in the RNA? Well, we might just blame it on the evolution process. RNA was first and DNA came later, and while U and T are very similar molecules, in biology a small difference in the chemical structure means a lot, and there are advantages and disadvantages on both T and U but after millions of years of evolution it seems it is OK to leave U in the RNA and T in the DNA. Not much of an explanation, but I am fine with that.

After the transcription, the mRNA can be sent out of the nucleus where it will be translated into a protein. In this process, there is another type of RNA, called transfer RNA, or tRNA, involved in the translation itself. This translation is the synthesis of a protein. And what does the tRNA do? It recognises a sequence of three bases from the RNA (which came from a complementary triplet in the DNA) and is capable to bring the corresponding amino acid. This means that from a code of 4 letters (A, C, T and G) we go to another code of similar letters (RNA has A, U, C and G), and from groups of three of these RNA bases we can translate to the 20 amino acids. This is the famous genetic code. There are synonyms, of course (if you know statistics, you may have realized that there are more than one base triplet that can encode for the same amino acid). And there are groups corresponding for the START and for the STOP messages.

So if a cell needs to produce collagen, for example, first there will be a messenger (generally it will be a peptide, a protein or a glycoprotein) being recognized by a specific receptor (typically, it will be a transmembrane protein or glycoprotein) which will trigger the signal which will then activate the gene expression (the process of transcription from DNA into mRNA, and afterwards the translation from mRNA to protein). After the protein synthesis, and back to the example of collagen, the synthesized collagen will be transported outside of the cell, as this protein is mainly structural for the medium outside of the cells (the extracellular matrix -ECM-, where collagen will also meet HA, a polysaccharide also present in the ECM). The biochemical machinery of the cell in action!

You see, we are made of polymers which have different functions and interact with each other. And as I said in a previous article, if life started with amino acids and proteins, one of the big mysteries is how come the information of proteins ended up stored in the DNA, with the intermediary RNA-phase in between. We know this has advantages, but not how it actually happened within the evolution (unless I have missed a very important advance in this direction I did not hear of).

We know that, like in programming we have the binary code of zeros and ones to encrypt the “words” of the software, it looks quite clever to encrypt 20 amino acids in only four nitrogenous bases (or nucleobases), and that in terms of space it is clever to coil the double helix into a smaller space so from that archive the cell machinery can access determined “files” (the genes) at precise moments, but the big question remains: how did the evolution manage to come up with such an elegant solution? And as I read recently (*), there are still so many things about life we don’t know yet…

Sunday, 17 November 2013

A Few Curiosities About The Solar System

I did not know all of this myself until I saw a couple of documentaries in which these curious things were explained. One never stops learning.

The first curious thing I want to explain today is that the size of the Solar System is quite a tricky topic. At school I just learned that the Solar System is composed by the Sun and the planets: Mercury, Venus, Earth, Mars, Jupiter, Saturn, Uranus, Neptune and Pluto. Later I learned that between Mars and Jupiter there is an asteroid belt. And then, in 2006, Pluto lost its category as a planet. Therefore, Neptune is the outermost planet of the Solar System. But the Solar System does not end in Neptune! It is much bigger than that!

If we were in a spaceship sent out towards the edge of the Solar System and continued travelling past the orbit of Neptune, we would eventually reach Pluto, or at least its orbit, and then other objects composed primarily of rock and ice. Pluto and the other objects form the Kuiper belt, a region extending from Neptune’s orbit, at 30 AU, to approximately 50 AU from the Sun.

To clarify the distances, 1 AU (astronomical unit) is the average distance from the Earth to the Sun: 150,000,000 (150 million) km, or 1.5 x 108 km. If we keep in mind that the orbit of the Earth is elliptical, when it is closer to the Sun our home world is at around 147 million km, and when our planet is farther it is at around 152 million km. So if we multiply the average, 150 million km, by 30 we get to the average distance between Neptune and the Sun: 30 AU, i.e., 4.5 x 109 km (a 45 followed by 8 zeros). And the Kuiper belt would end at 50 AU, i.e., at 7.5 x 109 km.

But still, if we had been able to travel with our spaceship that far, we would not be exiting the Solar System yet!

The point at which the Solar System ends and interstellar space begins is not precisely defined since its outer boundaries are shaped by two separate forces: the solar wind and the Sun's gravity. The outer limit of the solar wind's influence is roughly four times Pluto's distance from the Sun, which is considered the beginning of the interstellar medium. However, the Sun's effective range of gravitational dominance is believed to extend up to a thousand times farther.

Then there is also the Oort cloud, which is a hypothetical spherical cloud of up to a trillion icy objects that is believed to be the source for all long-period comets and to surround the Solar System at roughly 50,000 AU (around 1 light-year -ly-), and possibly to as far as 100,000 AU (1.87 ly). It is believed to be composed of comets that were ejected from the inner Solar System by gravitational interactions with the outer planets. Oort cloud objects move very slowly, and can be perturbed by infrequent events such as collisions, the gravitational effects of a passing star, or the galactic tide, the tidal force exerted by the Milky Way.

So, from our planet, at 1 AU from the Sun, and Neptune, at 30 AU from the Sun, we have gone as far as at least 105 AU!!! Isn’t it amazing? Our galactic district is much bigger than it seemed.

There are three other curious points I would like to mention. But now I would do a U-turn with our spaceship to go back home and have a closer look at the two closest neighbours of the good Earth, and to our planet as well.

If an observer could be placed above the Sun’s north pole, and had the capacity to see all the planets until Neptune, he would observe that the eight companions of the Sun orbit in an anti-clockwise direction from the viewing point. And he could also see that almost all the eight planets also rotate on their axis in an anti-clockwise direction (just like the Sun itself), but Venus and Uranus rotate clockwise. This is called “retrograde rotation”.

While I haven’t found a convincing and/or comprehensive explanation for these two exceptional retrograde rotations (OK, I have not done a deep research, but I guess that this is still being studied and the real explanation is yet to be found out), I saw in a documentary a plausible theory explaining the case of Venus: a huge mass impacted with Venus some millions of years ago, and the impact was so strong that it caused the planet to rotate in the other sense. Being the rotation of Venus the slowest in the system (it takes 243 Earth days, while its orbit around the Sun is faster, taking 224.7 Earth days), it looks quite a reasonable explanation to me. In any case, I find of significance the fact that out of 8 planets only 2 rotate in the different sense.

From Venus we move back to Earth for a while, and I would like to make a stop on the Moon as well. From Earth we always see the same face of the Moon. The explanation is quite simple: the same gravitational attraction between the Earth and the Moon which causes the tides on Earth does also cause that the Moon’s rotation period is the same as the time it takes to orbit the Earth. The Moon may have also dramatically affected the development of life on Earth by moderating our planet’s climate. And here we come to an interesting information regarding the Moon: how was it formed? Well, the most widely accepted theory of the Moon’s origin, the “giant impact theory”, states that it formed from the collision of a Mars-sized protoplanet with the early Earth. The Earth would have been smaller than it is now until that moment, and after the impact part of the protoplanet melted with Earth and the rest was expelled to become, first, a ring of rocks orbiting Earth and then, the Moon (gravity playing once again here). This hypothesis explains, among other things, the Moon’s relative lack of iron and volatile elements, and the fact that its composition is nearly identical to that of the Earth’s crust.

Our next excursion within the Solar System shall take us to Mars. It has always been a fascinating world for mankind, inspiring us and making us dream of the impossible. For now, I would just like to point it out that its mountains are so big and so high that if we stood in front of any of them we could not see it completely, so huge they are. Olympus Mons, the tallest mountain of the Solar System, is 22 km high, far above the 8.8 km height of Mount Everest on Earth. Similarly, the canyon Valles Marineris on Mars is much more impressive than the Grand Canyon of Colorado (but it is much easier for us to enjoy the latter!). It comes of no surprise Valles Marineris can be seen from space and is one distinctive characteristics of the Red Planet. It seems that Valles Marineris was formed from a combination of volcanic activity and asteroid impacts.

So with a size much bigger than one would initially think and many cosmic impacts along its history which gave shape to its planets and their corresponding satellites, the Solar System has a lot of mysteries for us yet to unveil. Who knows what other amazing stories are waiting for us out there...

Sunday, 13 October 2013

A Tale Of The Earth

The Solar System formed 4.6 billion years ago from the gravitational collapse of a region within a large interstellar cloud which was big enough to probably birth several stars. This formation of the Sun and the eight planets orbiting it took its time. For a start, 50 million years just for having, in the core of the protostar -an "embryo" of what would become the Sun-, a pressure and density of hydrogen high enough to begin the thermonuclear fusion -the conversion of hydrogen into helium, which is the reaction that releases the Sun's energy-.

Eventually, the Sun was born and then the 8 planets around it were born too. And no one would have ever said that in the third planet, at an average distance of 150 million km (147-152), a series of miracles would lead to the appearance of life. So life as we know it on Earth is nothing but an accident, or even most amazingly, a chain of accidents. Isn't it incredible?

Many things have happened on Earth for such an achievement. From one end, it seems that the planet is at a correct distance from the Sun: not too close and at the same time not too far, in order to have a suitable light and heat from the star, as well as a huge amount of water on liquid state (over 70% of the planet is covered by water, which contains about half of the planet's species). But this alone would not be enough, and on our planet things were not always so easy for the development of life. The geological history of the planet is full of challenges that life forms, and their very self-survival, had to deal with.

Earth's atmosphere and oceans formed by volcanic activity and outgassing that included water vapour. The origin of the world’s oceans was condensation augmented by water and ice delivered by asteroids, proto-planets and comets. Atmospheric “greenhouse gases” kept the oceans from freezing while the newly forming Sun was only at 70% luminosity. By 3.5 billion years ago, the Earth’s magnetic field was established, which helped prevent the atmosphere from being stripped away by the solar wind.

A crust formed when the molten outer layer of the planet Earth cooled to form a solid as the accumulated water vapour began to act in the atmosphere. Continents formed by plate tectonics, a process ultimately driven by the continuous loss of heat from the Earth's interior. On time scales lasting hundreds of millions of years, the supercontinents have formed and broken up three times.

The ice ages began about 40 million years ago and then intensified during the Pleistocene about 3 million years ago. High-latitude regions have since undergone repeated cycles of glaciation and thaw, repeating every 40–100,000 years. The last continental glaciation ended 10,000 years ago. There is a very curious (and important) correlation between the ice ages and the composition of the Earth's atmosphere, and also with some milestones of the evolution of life on Earth.

There was a moment when the atmosphere contained a lot of methane (about a 1000 times as much as there is now), which is a very strong greenhouse gas (it gives a greenhouse effect higher than that of carbon dioxide). This methane was generated by the volcanic activity and contributed to a quite warm temperature in the planet. As life evolved in the oceans and organisms able to do the photosynthesis appeared, oxygen was a harmful by-product which was released into the water and then it bubbled until it reached the atmosphere. 

What happens when oxygen meets methane? Methane burns, reacting with oxygen to produce carbon dioxide and water. So after a time, oxygen almost depleted the atmosphere from methane, and the temperature decreased very significantly. That was a hard period for life survival, but life did not disappear from the planet.

Another difficult period was the "Snowball Earth", in which the temperatures went very low once again, and almost the whole planet was covered by ice. If snow falls for a long time and layer on layer, it forms ice by compression. And the white colour reflects the light, so it makes the temperature go yet colder. The "Snowball Earth" lasted quite a long time, and still, life resisted. 

Eventually, the volcanic activity generated enough carbon dioxide which increased again the global temperature and finally melted the "snowball". After this melting, many multicellular life forms appeared on the planet, and this was accompanied by a new increase in the oxygen content of the atmosphere. It even got to a point with an atmosphere having 30% of oxygen for a time in which animals grew very big in size!

But what I find most amazing is, how did life actually begin?

Earth formed, like the other seven planets of the Solar System, by colliding masses that melted and got stuck together, and in the early times many more asteroids and comets came to meet Earth on their way. Blame it on the gravity. At a point, the different layers were established (nucleus, mantle and crust), and the volcanic activity began. The water vapour condensed (blame it, again, on the gravity) and rain fell to form the oceans. And once the oceans were on the surface of the planet, their water allowed many interesting chemical reactions to take place.

It is generally accepted that small molecules dissolved in the water formed the first amino acids (the building blocks of the proteins), and this was the starting point of it all. It is surprising that this happened to such a great extent, but to add a note of curiosity, Friedrich Wöhler synthesized, in 1828, urea (an organic compound) from ammonium cyanate (an inorganic substance), and in 1845 Hermann Kolbe did something similar by synthesizing acetic acid from carbon disulfide. So why would not react ammonia salts and other small inorganic molecules to form the amino acids (organic compounds) that are part of the proteins? Then, the amino acids would combine between themselves to form proteins, and these proteins would have particular three-dimensional structures which would allow specific functions. 

What would be the next step towards life? The definition of living organism includes “the capacity to self-replicate” (more extensively, “organisms are capable of responding to stimuli, reproduction, growth and development, and maintenance of homeostasis as a stable whole”). So here is one of the great mysteries of life: how is it possible to achieve a self-replicating complex form like a cell from just proteins?

In another post I will explain the relationship between the DNA and the proteins, but for the moment let’s say it kind of went in a "reverse mode". From the proteins, somehow the biological information was finally stored in another molecule, the DNA, which can be copied when the self-replication comes. The DNA has a constant structure, the double helix, as opposed to the many different structures that proteins can have, and it can be coiled and packed to store a lot of information in a much smaller space (the 3D structure of proteins make them quite big, and they need to keep that big 3D structure to be "operative"). So DNA has a great advantage in front of the proteins when it comes to storing information.

Then the complexity increased progressively. The different “biomolecules” (molecules present in the life forms) self-assembled first into cells to form unicellular organisms. The first unicellular organisms, called prokaryotes, were smaller cells and without a defined cell nucleus (the DNA was not in a separate compartment from the rest of components of the cell). Bacteriae are microorganisms that belong to the prokaryotes.

Later, some prokaryotes specialised and started living in symbiosis with larger cells, so the next milestone of the evolution was achieved: the appearance of eukaryotes. Eukaryotes are larger than prokaryotes, and have a nucleus which contains the DNA, as well as other different compartments for different functions.

And finally, as some eukaryotic cells within colonies (groups of cells) became increasingly specialised, the first multicellular organisms made their appearance. We belong to this last evolved group of organisms, but this does not mean that we are “superior organisms”...

Thursday, 10 October 2013


We live in a fascinating world within a fascinating universe. Yet we only know a very tiny part of the whole. The need to understand our environment is part of our nature. And here, in this corner of a neighbourhood called The Milky Way, the human being keeps on trying to enlarge the known fragment of the universe.

It might be a dream, but it would be a dream worth dreaming anyway. Our intrinsic curiosity has lead us to better understand, for example, the basics of life, the chemical structure at the atomic scale and below, the formation the Solar System and the incredible history of our planet.

Nowadays, the society seems not to care much about science. Fortunately, there are a lot of heroes who don't give up. Furthermore, science and technology have made possible for us to fly on an airplane while listening to music in our mp3 player or mobile phone, or reading on an e-book, or even working, to put just one example of so many I could think of. 

Sometimes the simple possibility to have a shower with running hot water could be a miracle if it weren't for the people who made that possible. So, many should thank science and engineering about a thousand times each day for every little miracle transformed into common reality. And even if we just were at the ape stage of the evolution process, we might just look at the miracles that nature can offer many times a minute (whenever there was no threat of a predator trying to have us for lunch, of course!).

So, science is the pathway to understanding what sorrounds us, which could actually mean everything from our own cells to the world we live in to the very most distant galaxy we have been able to identify so far. Anything! Then, why is it considered as something too boring to pay attention to most of the times? Or something out of which it is impossible to make a living of? Is it possible to understand well more or less complex scientific concepts?

I don't know the answer to the last question, as I don't know how many subjects I will be able to do my best to explain in a comprehensive way. I am not a teacher, but I studied Chemistry and Biochemistry, and one of my other passions, among which we can also find reading and listening to music, is astronomy (unfortunately, I never had time to learn about it, but every now and then I managed to read a few books on the subject). So I have a scientific background.

One of my "local heroes" is Eduard Punset, who can be counted among the great communicators of science to the public. In part as a homage to him, like I was trying to follow his path in a way (I know I am not him), I have decided to start this blog. Another reason is that I wanted to do something apart from my job, in my free time. And I am sure there are many other reasons for it, but I don't want to list them (I don't even know all of them!). Of course, a big question is how often will I be able to post. I will do my very best to find time for it, if not every week once or twice a month at least. We will see.

Nevermind, welcome to "Science At Hand"!

This is Raul Vallecillo, trying to bring science to everyone, inlcuding non-scientists. I come from Spain but I have chosen the English language for a more international and worldwide approach. Hope anyone landing here will have a chance to understand what I write, :-)