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On March 6, 1869, Dmitri Mendeleev’s breakthrough discovery was presented to the Russian Chemical Society. The chemist had determined that the known elements — 70 at the time — could be arranged by their atomic weights into a table that revealed that their physical properties followed regular patterns. He had invented the periodic table of elements.
In his early twenties, Mendeleev had intuited that the elements followed some kind of order, and he spent thirteen years trying to discover it. In developing his system, he drew on the data and ideas of scientists around the world. Two — Lothar Meyer and British chemist John Alexander Reina Newlands — had published ideas about the periodicity of elements. But Mendeleev’s addressed every known element, which theirs had not.
His system also surpassed the others because he accounted for gaps in the sequence of elements. Mendeleev said that an element would be discovered to fill each gap and even predicted the properties of those elements. The discovery of the one of these missing elements — gallium, in 1875 — helped spur wide acceptance of Mendeleev’s system.
Later work showed that Mendeleev’s reliance on atomic weight to determine periodicity is not completely correct. While atomic weight tends to increase as one moves from element to element, there are exceptions. Mendeleev also did not have the theoretical understanding to explain why the elements exhibited these periodic characteristics. Nevertheless, his achievement marked an important milestone in the understanding of the physical world.
Mendeleev did not personally present his breakthrough to the Chemical Society. Ill on the day of the meeting, he asked a colleague to deliver the report.
Interestingly, the date celebrated for this event reflects Russia’s use of the “Old Style” Julian calendar. According to the “New Style” Gregorian calendar — not adopted in Russia until after 1918 — Mendeleev’s periodic table was presented twelve days later, on March 18.
Every month OUP editor and author Jonathan Crowe answers your science questions in the monthly SciWhys column. Got a burning question about science that you’d like answered? Just email it to us, and Jonathan will answer what he can. Today: Why do we eat food?
By Jonathan Crowe
You may well be thinking that the question posed in the title of this blog has an all-too-obvious answer. We all know that we eat food to keep ourselves alive. But why do we find ourselves slaves to our appetites and rumbling stomachs? What is actually happening inside each of us that couldn’t happen without another slice of toast, or piece of fruit, or that most vaunted of mid-afternoon pick-me-ups, the sneakily-consumed bar of chocolate?
We’re all familiar with the concept of something needing fuel to keep it going. Just as a power station requires gas or coal to power its turbines and generate energy, so we need fuel – in the form of food – to power our continued existence.
The foods we eat provide us with a range of nutrients: vitamins, minerals, water, fat, carbohydrates, fibre, and protein. These nutrients are put to different uses — as building materials to construct the tissues and organs from which our bodies are made; as the components of the molecular machinery that keeps our cells running as they should. All of these uses are unified by a common theme: a requirement for energy to make them happen. And this is where one particular type of nutrient comes into its own. Step forward the carbohydrates.
Carbohydrates are better known to us as sugars, but in fact the sweet crystals we know as sugar are only part of this group. Carbohydrates come in very different shapes and sizes. One of the smallest is glucose, which acts as a chemical building block — multiple copies of glucose can join together to form a range of much larger molecules. For example, starch – found in potatoes and flour – is a carbohydrate formed from many individual molecules of glucose joined together in long chains. (Based on taste alone, you wouldn’t think that starch was made of glucose. Even though individual molecules of glucose taste sweet to us, once they are linked together to form starch the sweetness is lost.)
To understand how the sugar in our food can power the processes occurring in our cells every minute of every day, let’s follow some starch on its journey through the body. Many of the foods we consume aren’t in a form with which our bodies can do anything useful. Instead, they need to be digested. And so it is with carbohydrates such as starch. This process of digestion starts as soon as the food enters our mouth; our saliva contains special substances (called enzymes) that start attacking the long chains of starch, breaking it into smaller fragments.
Digestion continues as our food is swallowed and slides down into our stomach, where an arsenal of other chemical weapons set to work on the mouthful we’ve just consumed. Before long, what were initially mouth-watering morsels are reduced to something rather less appetising and leave the stomach to enter the long, snaking tunnel of our intestines. By now, the long chains of starch have been broken down into glucose, which is small enough to pass through the lining of our intestine and into our bloodstream. Our bloodstream acts as a short- and long-distance transport network, carrying the newly-arrived sugar molecules to cells all over the body.
When glucose arrives at its destination and first enters the cell, it u
By Jonathan Crowe
Each day of our lives is a battle for survival against an army of invaders so vast in size that it outnumbers the human population hugely. Yet, despite its vastness, this army is an invisible threat, each individual so small that it cannot be seen with the naked eye. These are the microbes – among them the bacteria and viruses – that surround us every day, and could in one way or another kill us were it not for our immune system, an ingenious defence mechanism that protects us from these invisible foes.
This is the latest post in our regular OUPblog column SciWhys. Every month OUP editor and author Jonathan Crowe will be answering your science questions. Got a burning question about science that you’d like answered? Just email it to us, and Jonathan will answer what he can. Today: how do organisms evolve?
By Jonathan Crowe
The world around us has been in a state of constant change for millions of years: mountains have been thrust skywards as the plates that make up the Earth’s surface crash against each other; huge glaciers have sculpted valleys into the landscape; arid deserts have replaced fertile grasslands as rain patterns have changed. But the living organisms that populate this world are just as dynamic: as environments have changed, so too has the plethora of creatures inhabiting them. But how do creatures change to keep step with the world in which they live? The answer lies in the process of evolution.
Many organisms are uniquely suited to their environment: polar bears have layers of fur and fat to insulate them from the bitter Arctic cold; camels have hooves with broad leathery pads to enable them to walk on desert sand. These so-called adaptations – characteristics that tailor a creature to its environment – do not develop overnight: a giraffe that is moved to a savannah with unusually tall trees won’t suddenly grow a longer neck to be able to reach the far-away leaves. Instead, adaptations develop over many generations. This process of gradual change to make you better suited to your environment is called what’s called evolution.
So how does this change actually happen? In previous posts I’ve explored how the information in our genomes acts as the recipe for the cells, tissues and organs from which we’re constructed. If we are somehow changing to suit our environment, then our genes must be changing too. But there isn’t some mysterious process through which our genes ‘know’ how to change: if an organism finds its environment turning cold, its genome won’t magically change so that it now includes a new recipe for the growth of extra fur to keep it warm. Instead, the raw ‘fuel’ for genetic change is an entirely random process: the process of gene mutation.
In my last post, I considered how gene mutation alters the DNA sequence of a gene, and so alters the information stored by that gene. If you change a recipe when cooking, the end product will be different. And so it is with our genome: if the information stored in our genome – the recipe for our existence – changes, then we must change in some way too.
I mentioned above how the process of mutation is random. A mutation may be introduced when an incorrect DNA ‘letter’ is inserted into a growing chain as a chromosome is being copied: instead of manufacturing a stretch of DNA with the sequence ATTGCCT, an error may occur at the second position, to give AATGCCT. But it’s just as likely that an error could have been introduced at the sixth position instead of the second, with ATTGCCT becoming ATTGCGT. Such mutations are entirely down to chance.
And this is where we encounter something of a paradox. Though the mutations that occur in our genes to fuel the process of evolution do so at random, evolution itself is anything but random. So how can we reconcile this seeming conflict?
To answer this question, let’s imagine a population of sheep, all of whom have a woolly coat of similar thickness. Quite by chance, a gene in one of the sheep in the population picks up a mutation so that offspring of that sheep develop a slightly thicker coat. However, the thick-coated sheep is in a minority: most of the population carry the normal, non-mutated gene, and so have coats of normal thickness. Now, the sheep population live in a fairly tempera
I wonder how many times students have been directed to complete a table for homework or on an exam. Chemists have an incomplete table that they are trying to complete: the Periodic Table of the Elements, or the Periodic Table, for short. Uranium, element number 92 is the last naturally occurring element in the Periodic Table. Elements beyond number 92, called the transuranium elements, have all been produced in laboratories. The first transuranium element, neptunium (#93) was produced in 1940 at the University of California, Berkeley, by Edwin McMillan and Phillip Abelson by exposing uranium oxide to neutrons from a cyclotron. The last one, copernicium (#112) was officially recognized in 2009.
On June 6, 2011, the Joint Working Party on the Discovery of Elements of the International Union of Pure and Applied Chemistry (IUPAC) and the International Union of Pure and Applied Physics (IUPAP) announced the addition of two new elements to the Periodic Table—element 114 and element 116. For now, element 114 is called ununquadium and element 116 is called ununhexium. These names are based on their atomic numbers. By officially acknowledging the collaboration between researchers from Lawrence-Livermore National Laboratory in California and Russia’s Joint Institute for Nuclear Research in Dubna, these researchers will get to suggest names for the new elements. The names will go through a review process before being adopted and the elements will be assigned a symbol by the IUPAC Council.
Scientists produced these elements by bombarding curium (#96) atoms with calcium (#20) nuclei. In a few milliseconds, element 116 decays into element 114 which lasts about half a second before decaying into copernicium (#112). In other experiments element 114 was produced by bombarding plutonium (#94) with calcium nuclei. Notice that 96 + 20 = 116 and 94 + 20 = 114.
There are three more elements waiting to be recognized: 113, 115, and 118. According to IUPAC, “Review of the claims associated with elements 113, 115, and 118 are at this time not conclusive and evidences have not met the criteria for discovery.” As soon as I hear anything more, I will let you know.
So far, 2010 has been an exciting year for chemists, and it’s only April. The International Union of Pure and Applied Chemistry (IUPAC) announced the name chosen for the human-made element formerly known as ununbium. That’s element number 112 on the Periodic Table of the Elements and its symbol was Uub. By the way, the name and symbol were derived from the Latin version of the element’s atomic number, 112. The element’s formal name is copernicium and its symbol is Cn. The IUPAC made the announcement on February 19, which was the 537th anniversary of the birth of Nicolas Copernicus, for whom the element was named.
Although the IUPAC makes the final decision, it gives the first researchers to produce a new element the honor of proposing its name. Many of the human-made elements are named after famous scientists. For example: Es, element 99, einsteinium, after Albert Einstein; Sg, element 160, seaborgium, after Glenn Seaborg, an American physicist. Other human-made elements are named for the place where they were discovered. For example: Bk, element 97, berkelium, after Berkley, California, where it was first produced; Db, element 106, Dubnium, after Dubna in Russia, where it was first produced; Ds, element 110, darmstatium, after Darmstadt, Germany, where it was first produced.
Copernicium was first produced by an international team of chemists on February 9, 1996 by bombarding a lead (atomic number 82) target with zinc ions (atomic number 30). The result was a new element with the atomic number 112. Copernicium falls below zinc, cadmium, and mercury on the Periodic Table of the Elements, making it part of Group 12 and a transition metal.
On April 7, a team of Russian and American scientists announced the production of element 117. For now, element 117 will be known as ununseptium and its symbol will be Uus. In a particle accelerator located in about 75 miles north of Moscow, scientists produce the six atoms of the new element by smashing together isotopes of calcium (atomic number 20) and berkelium (atomic number 97). Until the discovery is confirmed by other labs, the IUPAC will not give element 117 a formal name. Uus falls below astatine in the Periodic Table of the Elements, which makes it part of Group 17, the halogens.
I was reading an advertisement for athletic clothing that featured dry-wick fabric. I have heard my son Don, the runner, extol the virtues of dry-wicking tee shirts and shorts. The idea is that these fabrics will keep you cool, dry, and comfortable no matter how hard you exercise. What’s the science behind how they work and what are they made of, I wondered. The answer arrived a few days later in an article from the Washington Post.
According to the article, it all depends on the fibers the fabric is made of. For example, natural fibers, such as cotton, are very good at absorbing moisture. However, they are not very good at letting go of moisture, that is letting the sweat evaporate from the fabric. On the other hand, polyester is not good at absorbing moisture; it will trap heat and moisture on your body. Now nylon, also a synthetic fiber, is pretty good at absorbing moisture and also pretty good at letting go of it, which is why nylon garments dry quickly.
To make dry-wick 100 percent polyester fabric, manufacturers can add a coating to the fibers, adjust the chemistry of the polyester fibers, or change their shape to make them more absorbent. Most polyester fibers are tube-shaped, but giving them a scalloped-oval or four-leaf-clover cross section makes them more absorbent because that creates tiny channels for the sweat to flow through to reach the outside of the fabric. (For you Earth science teachers, it is just like capillary action in soil.) Manufacturers can also mix natural fibers with synthetic fibers so that the fabric is absorbent, wicking the sweat away from your body and releasing the moisture from the surface of the fabric.
Unfortunately, there are no industry-wide standards for rating the moisture-wicking ability of clothes. Athletes, even weekend athletes, will have to figure out what they want from their workout clothes and read the labels. I guess that I don’t have to “sweat it,” because at my age, I rarely exercise that strenuously.
Many years ago, I went whale watching off Cape Cod, MA. It was a wonderful experience; seeing whales up close in their natural environment is certainly awe-inspiring. I knew that the species of baleen whales I saw (humpbacks and finbacks) are mainly plankton eaters, feeding on tiny crustaceans such as krill. I did not bother to think about the end product of that diet. But it seems that a conservation biologist named Joe Roman has done just that, and he claims that he has discovered an important step in one of the nutrient cycles in the sea.
People who have gardens may know about the element nitrogen; and people who have pets may know about diets containing amino acids and protein. The element nitrogen is an important component of amino acids. Chains of amino acids are the substances that make up proteins. And proteins, of course, are the nutrients that make up living things. So, nitrogen is an important element in natural cycles. Roman points out that algae (the base of the ocean food chain) living near the surface of the sea use up nitrogen as they grow and then take this element with them as they die and sink to the ocean floor. The same goes for fish, which eat the algae; except that the nitrogen they release is in their wastes, and that too sinks down in the ocean. So, for Roman, the question remained: How does nitrogen get back into the system, closer to the sea surface?
According to Roman, who watched whales as part of his research, some of this nitrogen returns to the surface when whales (which often feed in the depths) defecate and their waste products float near the surface. He contends that this whale waste, which is rich in nitrogen, helps fertilize more algae, which then helps feed more fish. And the cycle continues.
What links a queen honeybee to a particular group of four atoms (one carbon and three hydrogen atoms, to be precise)? The answer lies in the burgeoning field of epigenetics, which has revolutionized our understanding of how biological information is transmitted from one generation to the next.
The genetic information stored in our genome – the set of chromosomes that we inherit from our parents – directs the way in which we develop and behave. (We call the attributes and behaviours exhibited by an organism its ‘phenotype’.) Traditionally, the genetic information was thought to be encoded solely in the sequence of the four different chemical building blocks from which our DNA is constructed (that is, our genome sequence). If a DNA sequence changes, so the resulting phenotype changes too. (This is why identical twins, with genomes whose DNA sequences are identical, look the same, but other individuals, whose genomes comprise different DNA sequences, do not.) However, the field of epigenetics opens up a strong challenge to this traditional view of our DNA sequence being the sole dictator of phenotype.
So what actually is epigenetics? In broad terms, epigenetics refers to the way that the information carried in our genome – and the phenotype that results when this information is ‘deciphered’– can be modified not by changes in DNA sequence, but by chemical modifications either to the DNA itself, or to the special group of proteins called histones that associate with DNA in the cell. (It’s a bit like taking a book, with a story told in the author’s words, and adding notes on the page that alter how the story is interpreted by the next person to read it.)
But what has epigenetics to do with the group of four atoms, the one carbon and three hydrogen atoms mentioned at the start of this blog post? These four atoms can combine to form a methyl group – a central carbon atom, with three hydrogen atoms attached; the addition of methyl groups to both DNA and histone proteins in a process called methylation is a primary way in which epigenetic modification occurs. For example, the addition of a methyl group to one of the four chemical building blocks of DNA (called cytosine, C) either when it appears in the sequence CG (where G is the building block called guanine) or the sequence CNG (where N represents any of the four chemical building blocks of DNA) appears to result in that stretch of DNA being ‘switched off’. Consequently, the information stored in that stretch of DNA is not actively used by the cell; that stretch of DNA falls silent.
But what of our queen honeybee? Where does she fit into our story? A queen honeybee has an identical DNA sequence to her workers. Yet she bears some striking differences to them in terms of physical appearance and behavior (amongst other attributes). These differences are more than just skin-deep, however: the pattern of methylation between queen and worker larvae differs. Their genomes may be the same at the level of DNA sequence, but their different patterns of methylation direct different fates: the queen honeybee and her workers develop into quite distinct organisms.
Things take an interesting turn when we consider the cause of these different methylation patterns: the diets that the queen and workers experience during their development. The queen is fed on large quantities of royal jelly into adulthood, while worker larvae face a more meager feast, being switched to a diet of pollen and nectar early on. It is these diets that influence the way in which the queen and worker bees’ genes are switched on and off.
It is not just the queen honeybee whose genome is affected by the environment (in her case, diet). Mice exposed to certain chemicals during pregnancy have be
It began with the sound of a tyre rim grinding on the surface of the cycle path I’d been travelling along, and a sudden sensation of being on a bike that was moving through treacle rather than through air. My rear tyre had punctured and, not for the first time of late, I found myself resenting the seeming futility of life: of having the bad luck to get the puncture, of having to spend time and effort buying and fitting a new inner tube – of my life being enriched not one iota by the whole experience.
As I trudged home that evening, wheeling the now-useless bike beside me, I reflected on the many situations we encounter that mirror this experience – when we find ourselves having to invest energy, only to be no further forward, in real terms, having done so.
Why is it that we have to invest energy merely to maintain the status quo? Why do we find ourselves running, effectively only to stand still? The answer lies in an intrinsic property of all matter, a universal truth so fundamental to our existence that it is captured by its own law: the Second Law of Thermodynamics. This law tells us, in a nutshell, that we are living in a perpetual downward spiral, in which things just get worse. A cheery outlook on life, if ever there was one. But it is an outlook from which there is no escape: the universe, and everything in it, is gradually crumbling into a state of ever-increasing disorder.
This property of all matter – this collapse into disorder – is given a name: entropy. Things that are disordered have greater entropy than things that are relatively more organized. A glass of water, in which the molecules of water itself can move around relatively freely, is more disorganized – has greater entropy – than a block of ice, in which the molecules of water are trapped into a rigid, organized array.
A process that increases disorder, with its associated increase in entropy, is a spontaneous one: one that happens without having to do work to bring it about. This fact has one important corollary: a decrease in entropy – a move towards a more organized state – requires us doing work to bring it about. This is arguably why housework feels like a chore: a living room doesn’t spontaneously tidy itself. We need to invest effort to reverse the spread of disorder, and bring order to whatever degree of chaos had befallen our living space since we last made the effort to tidy up. We are essentially swimming against the natural tide of entropy, with disorder setting in the moment we take our foot off the pedal.
When we look at life at the scale of the molecules and cells of our bodies we continue to see an ongoing battle with entropy: a tussle between order and disorder. Consider proteins, the molecular machines that carry out many important functions in the cell. As they are first being manufactured (or ‘synthesised’) in the cell, proteins exist as elongated chains of conjoined amino acid subunits, much like links of sausages as they are extruded from a sausage-making machine. However, these elongated protein chains must fold into specific three-dimensional shapes to function correctly. This folding represents an increase in order, and hence a decrease in entropy. As we note above, though, swimming against the tide of entropy comes at a cost: the cell must do work to drive such a process forward.
This battle against entropy is essentially why we must eat on a regular basis: to give the cells of our body the energy they need to drive forward those processes that won’t happen spontaneously.
Even the very continuation of life is a battle against disorder. Successful reproduction relies on the passing of biological information from one generation to the next. Every time a cell divides, it must pass on a copy of its
Today we’d like to introduce our latest regular OUPblog column: SciWhys. Every month OUP editor and author Jonathan Crowe will be answering your science questions. Got a burning question about science that you’d like answered? Just email it to us, and Jonathan will answer what he can. Kicking us off: What is DNA and what does it do?
By Jonathan Crowe
We’ve all heard of DNA, and probably know that it’s ‘something to do with our genes’. But what actually is DNA, and what does it do? At the level of chemistry, DNA – or deoxyribonucleic acid, to give it its full name – is a collection of carbon, hydrogen, oxygen, nitrogen and phosphorus atoms, joined together to form a large molecule. There is nothing that special about the atoms found in a molecule of DNA: they are no different from the atoms found in the thousands of other molecules from which the human body is made. What makes DNA special, though, is its biological role: DNA stores information – specifically, the information needed by a living organism to direct its correct growth and function.
But how does DNA, simply a collection of just a few different types of atom, actually store information? To answer this question, we need to consider the structure of DNA in a little more detail. DNA is like a long, thin chain – a chain that is constructed from a series of building blocks joined end-to-end. (In fact, a molecule of DNA features two chains, which line up side-by-side. But we only need to focus on one of these chains to be able to understand how DNA stores its information.)
There are only four different building blocks; these are represented by the letters A, C, G and T. (Each building block has three component parts; one of these parts is made up of one of four molecules: adenine, cytosine, guanine or thymine. It is these names that give rise to letters used to represent the four complete building blocks themselves.) A single DNA molecule is composed of a mixture of these four building blocks, joined together one by one to form a long chain – and it is the order in which the four building blocks are joined together along the DNA chain that lies at the heart of DNA’s information-storing capability.
The order in which the four building blocks appear along a DNA molecule determines what we call its ‘sequence’; this sequence is represented using the single-letter shorthand mentioned above. If we imagine that we had a very small DNA molecule that is composed of just eight building blocks, and these blocks were joined together in the order cytosine-adenine-cytosine-guanine-guanine-thymine-adenine-cytosine, the sequence of this DNA molecule would be CACGGTAC.
The biological information stored in a DNA molecule depends upon the order of its building blocks – that is, its sequence. If a DNA sequence changes, so too does the information it contains. On reflection, this concept – that the order in which a selection of items appears in a linear sequence affects the information stored in that sequence – may not be as alien to us as it might first seem. Indeed, it is the concept on which written communication is based: each sentence in this blog post is composed of a selection of items – the letters of the alphabet – appearing in different sequences. These different sequences of letters spell out different words, which convey different information to the reader.
And so it is with the sequence of DNA: as the sequence of the four building blocks of DNA varies, so too does the information being conveyed. (You may well be asking how the information stored in DNA is actually interpreted – how it actually determines how an organism develops and functions – but that’s a topic for a different blog post.)
This is the second post in our latest regular OUPblog column: SciWhys. Every month OUP editor and author Jonathan Crowe will be answering your science questions. Got a burning question about science that you’d like answered? Just email it to us, and Jonathan will answer what he can. Today: What are genes and genomes?
By Jonathan Crowe
I described in my last blog post how DNA acts as a store of biological information – information that serves as a set of instructions that direct our growth and function. Indeed, we could consider DNA to be the biological equivalent of a library – another repository of information with which we’re all probably much more familiar. The information we find in a library isn’t present in one huge tome, however. Rather, it is divided into discrete packages of information – namely books. And so it is with DNA: the biological information it stores isn’t captured in a single, huge molecule, but is divided into separate entities called chromosomes – the biological equivalent of individual books in a library.
I commented previously that DNA is composed of a long chain of four building blocks, A, C, G, and T. Rather than existing as an extended chain (like a stretched out length of rope), the DNA in a chromosome is tightly packaged. In fact, if stretched out (like our piece of rope), the DNA in a single chromosome would be around 2-8 cm long. Yet a typical chromosome is just 0.00002–0.002 cm long: that’s between 1000 and 100,000 times shorter than the unpackaged DNA would be. This packaging is quite the feat of space-saving efficiency.
Let’s return to our imaginary library of books. The information in a book isn’t presented as one long uninterrupted sequence of words. Rather, the information is divided into chapters. When we want to find out something from a book – to extract some specific information from it – we don’t read the whole thing cover-to-cover. Instead, we may just read a single chapter. In a fortuitous extension of our analogy, the same is true of information retrieval from chromosomes. The information captured in a single chromosome is stored in discrete ‘chunks’ (just as a book is divided into chapters), and these chunks can be read separately from one another. These ‘chunks’ – these discrete units of information – are what we call ‘genes’. In essence, one gene contains one snippet of biological information.
I’ve just likened chromosomes to books in a library. But is there a biological equivalent of the library itself? Well, yes, there is. Virtually every cell in the human body (with specific exceptions) contains 46 chromosomes – 23 from each of its parents. All of the genes found in this ‘library’ of chromosomes are collectively termed the ‘genome’. Put another way, a genome is a collection of all the genes found in a particular organism.
Different organisms have different-sized genomes. For example, the human genome comprises around 20,000-25,000 genes; the mouse genome, with 40 chromosomes, comprises a similar number of individual genes. However, the bacterium H. influenzae has just a single chromosome, containing around 1700 genes.
It is not just the number of genes (and chromosomes) in the genome that varies between organisms: the long stretches of DNA making up the genomes of different organisms have different sequences (and so store different information). These differences make sense, particularly if we imagine the genome of an organism to represent the ‘recipe’ for that organism: a human is quite a different organism from a mouse, so we would expect the instructions that direct the growth and function of the two organisms to differ.
This is the third post in our latest regular OUPblog column: SciWhys. Every month OUP editor and author Jonathan Crowe will be answering your science questions. Got a burning question about science that you’d like answered? Just email it to us, and Jonathan will answer what he can. Today: How is the information in a gene used by a cell?
By Jonathan Crowe
In my last twoposts I’ve introduced the notion that DNA acts as a store of biological information; this information is stored in a series of chromosomes, each of which are divided into a number of genes. Each gene in turn contains one ‘snippet’ of biological information. But how are these genes actually used? How is the information stored in these genes actually extracted to do something useful (if ‘useful’ isn’t too flippant a term for something that the very continuation of life depends upon).
Many (but not all) genes act as recipes for a family of biological molecules called proteins: they literally tell the cell what the ingredients for a particular protein are, and how they should be combined to create the protein itself. (Proteins have a range of essential roles in the human body. Some act as building materials for different components of the body, such as the keratin we find in our hair and nails. Others act as molecular transporters: haemoglobin, which is found in our red blood cells, carries oxygen from our lungs to other parts of the body. A family of proteins called the enzymes are arguably the most important, however. Enzymes cajole different chemicals in our body into reacting with one another. Without enzymes, our bodies would be unable to generate energy from the food we eat (and you’d not be reading this blog post).)
So, somehow, the information stored in a DNA molecule is deciphered by the cell and used as the recipe for a protein. But how?
To answer this question, let’s take a journey inside the cell. We can imagine a cell to be like a factory, but one that has been divided into a series of physically separated compartments. Unlike a factory filled with air, a cell is filled with a jelly-like fluid called the cytoplasm, which surrounds the various compartments enclosed within it. In an earlier post I likened a genome to a biological library. And, inside the cell, this library is stored within a particular compartment called the nucleus.
I mentioned earlier that genes often act as recipes for proteins. But here comes a bit of a quandary: chromosomes – and the genes they contain – are locked away inside the cell’s nucleus. By contrast, proteins are manufactured by the cell in the cytoplasm, outside of the nucleus. So, for the genetic information to be used, it has to get out of nucleus and into the cytoplasm. How does this happen? Well, if we’re in a library with a book that contains information we really need, but we’re unable to take the book out of the library, we might make a photocopy of the page that holds the information we’re after. To get the information it needs out of the nucleus and into the cytoplasm the cell does something remarkably similar. The chromosome containing the gene of interest has to stay inside the nucleus, so the cell makes a copy of the gene – and that copy is then transported to where it is to be used: out of the nucleus and into the cytoplasm.
The copy of the gene generated during this cellular photocopying is made not of DNA but of a close cousin called RNA. RNA is made of three of the same building blocks as DNA – A, C and G. Instead of the T found in DNA, however, RNA uses a different block represented by the letter U (for ‘uracil’). Despite this
This is the latest post in our regular OUPblog column SciWhys. Every month OUP editor and author Jonathan Crowe will be answering your science questions. Got a burning question about science that you’d like answered? Just email it to us, and Jonathan will answer what he can. Today: what is gene mutation?
By Jonathan Crowe
In my last three posts I’ve introduced you to the world of biological information, taking you from the storage of biological information in libraries called genomes, which house information in individual books called chromosomes (themselves divided into chapters called genes), to the way the cell makes use of that stored information to manufacture the molecular machines called proteins.
But what happens when the storage of information goes wrong? If we’re reading a recipe and that recipe contains a mistake, chances are that the end-result of our culinary endeavour won’t end up as it should. And so it is at the level of cells. If the information the cell is using is somehow wrong, the end result will also be wrong – sometimes with catastrophic results.
I’ve mentioned in previous posts how biological information is captured by the sequence of the building block ‘letters’ from which DNA is constructed. The sequence of letters is ultimately deciphered by a molecular machine called the ribosome, which reads the sequence of letters in sets of three, and uses each trio to determine which amino acid – the building block of proteins – should be used next in its mission to construct a particular protein. It should come as no surprise that, if the recipe for the protein is changed – if the sequence of DNA ‘letters’ is altered – the protein that is manufactured will probably contain errors as a result. And if a protein contains errors, it won’t be able to function correctly, just as flat-packed furniture will end up being decidedly wobbly if you construct it from the wrong parts.
Imagine a snippet of DNA has the sequence GGTGCTAAG. The ribosome would ‘read’ this sequence, and would use it as the recipe for building a chain of three amino acids: Glycine-Alanine-Lysine. Now imagine that we alter just one letter in our original sequence so that it becomes GGTCCTAAG. All we’ve done is swap a G for a C at the fourth position in the DNA sequence. However, this change is sufficient to affect the composition of the protein that is produced when the sequence is deciphered: the ribosome will now build a chain with the composition Glycine-Proline-Lysine.
Surely such a small change won’t actually cause significant problems in a cell, though. Right? Wrong. Amazingly (and perhaps unnervingly) the tiniest error can have really quite significant consequences.
Let’s take just one example. Sickle cell anaemia is a condition that affects the red blood cells of humans. Red blood cells fulfil the essential role of transporting oxygen from our lungs to all the living cells of our body: they continually circulate through our arteries and veins, shuttling oxygen from one place to another. A healthy red blood cell looks a bit like a ring doughnut (though it doesn’t actually have a hole right through the middle); by contrast, the red blood cells of individuals with sickle cell anaemia become warped into crescent-like shapes (like a sickle, the grass-cutting tool, after which the disease is named). These sickle cells no longer pass freely through our arteries and veins. Instead, they tend to get entangled with each other. As a result, the flow of oxygen round the body is impeded, and
More apologies. I've been meaning to post links to all of Harold McGee's "Curious Cook" columns in The New York Times but fell down on the job. I was reminded by yesterday's column, so below is the list. Once again, you need to register to read NY Times articles, but registration is free.
Believe it or not, there is a kind of ice that burns. Called methane hydrate, chunks of this icy material will readily burst into flames simply by holding a lit match to them. Methane hydrate is a frozen substance made up of a single molecule of methane—a highly flammable gas—trapped within a lattice (a cagelike structure) formed by six water molecules. It is the most common form of a group of substances called gas hydrates, also known as clathrates.
Discovered in 1810 by British scientist Sir Humphrey Davy, gas hydrates were at first considered merely a laboratory curiosity. In the 1960s and 1970s, methane hydrates were encountered in nature during exploratory drilling for oil and natural gas and research drilling by oceanographers. Drillers initially tried to avoid methane hydrate deposits because of the possible dangers they posed to drilling rigs. However, since methane is the main component of natural gas, a fossil fuel used for power generation, heating and cooking, people soon realized that methane hydrate might constitute an important energy resource.
Methane hydrate is stable only under conditions of high pressure and low temperature. Deposits of the substance occur in ocean floor sediments on continental slopes, at water depths of at least 300 meters. In addition, it is found underground in areas of permafrost (permanently frozen ground) in places at high latitudes, such as Alaska and Siberia. Bacteria produce the methane as they break down the remains of dead organisms. The water that forms the icy cage surrounding the methane is present in the pore spaces between grains of soil or sediment.
Like vampires who turn to ash when exposed to sunlight, methane hydrate disintegrates rapidly under the environmental conditions at Earth’s surface. Because of this, scientists have had a difficult time studying this elusive substance. During early attempts to retrieve methane hydrates from the ocean depths at which they are stable, the icy chunks would melt and release gas as they neared the water’s surface, fizzing away like big seltzer tablets.
Nevertheless, a lot of research has been done since the early 1990s, and scientists have found that methane hydrate deposits are widespread in the world’s oceans. Vast deposits have been located of the east and west coasts of the United States, off the costs of northern Europe, near Japan, India, and many other places. Even the Black Sea south of Russia is thought to hold deposits of methane hydrate. Recent estimates suggest that global methane hydrate deposits may hold as much ad 10,000 gigatons (10,000 billion tons) of carbon. That is more than twice the amount of carbon believed to be stored in Earth’s reserves of petroleum, coal, and natural gas combined! If engineers can devise safe and cost-effective ways to recover methane hydrate from the ocean depths and permafrost regions, the future of this ice that burns looks bright indeed.
However, methane hydrate also has a dark side. Methane is a greenhouse gas, that is, a gas that traps the sun’s heat within the atmosphere, contributing to global warming. Although carbon dioxide is the main greenhouse gas of concern, methane is more than twenty times more efficient at trapping heat than is carbon dioxide. A sudden release of a large amount of methane, perhaps resulting from attempts to exploit methane hydrate deposits, could greatly accelerate global warming. In fact, some scientists believe that major releases of methane from underwater hydrate deposits, caused by natural events, were involved in past episodes of global warming and may even be linked to mass extinctions.
Consider the following scenario: methane hydrate deposits in sediments on continental slopes, the relatively steep areas between continental shelves and the deep ocean floor, make these slopes unstable. If an earthquake set off an underwater landslide, the sudden removal of the overlying material would allow methane hydrate to decompose, releasing methane gas. Some of the methane would rise up through the water and escape into the atmosphere, warming the climate and making life difficult for organisms adapted to cooler temperatures. The methane remaining in the ocean water would react chemically with dissolved oxygen in the water to form carbon dioxide, depriving marine animals of the oxygen they need to live These changes could cause some species to become extinct.
Alternatively, methane hydrate deposits could themselves cause an underwater landslide. For instance, lowering of sea level could reduce the pressure on methane hydrate deposits, allowing some to break down into water and gas. These fluids would weaken the sediments on continental slopes so that the slopes collapse, freeing methane from the remaining hydrate.
This is what scientists believe happened off the coast of Norway after the end of the last Ice Age. The massive Storegga Slide, which occurred about 7300 years ago is believed to have been triggered by a drop in sea level. In this colossal event, about 5500 cubic kilometers of sediment slid down the continental slope near Norway, traveling as far as 800 kilometers across the ocean floor. The slide caused the release of billions of tons of methane, producing a brief warming of the climate, and generating huge 20-meter tall waves called tsunamis, that ravaged the coasts of Scotland and Norway. Global warming, mass extinctions, underwater landslides, and giant waves—what else can be blamed on methane hydrate?
How about the Bermuda Triangle? This is not a joke; some people including scientists have speculated that the mysterious disappearances of ships in the area of the Atlantic Ocean bounded by Bermuda, Puerto Rico, and Florida, nicknamed the Bermuda Triangle, or Devil’s Triangle, could be related to sudden releases of methane gas from methane hydrate deposits. The thinking is that a sudden burst of gas would create a rising plume o bubbly, frothy water so low in density that it would be incapable of supporting any ship unlucky enough to be floating above the plume. The ship would sink like a stone, going straight toward the bottom without evening giving the crew time to send out a distress call.
Other scientists, while acknowledging that this is possible, point out that the odds of a ship being in the right (wrong?) place at the exact moment a plume of methane bubbles reaches the surface are extremely small. They also note that the greatest concentration of methane hydrate deposits within the Bermuda Triangle, at a seafloor feature called the Blake Ridge off the coast of South Carolina, is not an area where most ships have been reported missing. Moreover, there are many who believe that the whole Bermuda Triangle Theory is a myth; that statistical analyses show that no more ships have been lost there than in other heavily trafficked areas of the ocean.
Whatever the truth may be regarding the Bermuda Triangle, there is little doubt that methane hydrate will continue to be the focus of intense study by scientists, energy companies, and others in the years to come.
The above is an example of one of the Science, Technology, and Society features written by Jonathan Kolleeny for Reviewing Earth Science: The Physical Setting by Thomas McGuire. These features, found in the Answer Key, provide material for thought-provoking discussions with your class.
When I taught at the Windsor School, a private 7–12 school in Queens, some 20 years ago, each grade covered one science subject. In grade seven it was pre-Earth science, in grade eight it was pre-biology, and in grade nine it was pre-chemistry. This worked just fine at that time. Students were exposed to each of the high-school-level sciences that would be offered to them in grades 10, 11, and 12.
However, things in education have changed since then. Many states, including New York, now have an eighth-grade exam that tests the entire middle school science curriculum. After studying one science per year, how many students, I wonder, will be able to remember what they learned in the first year of middle school through to the last year? To me, the solution is to cover some life science, some physical science, and some Earth science each year in a curriculum that spirals through the grades.
To help teachers and students, Amsco has just published Amsco’s Science: Grade 8, the third volume of our three-book middle school science series. Its purpose is to provide a complete, clear, and concise presentation of middle school science concepts, in life, Earth, and physical science in an integrated approach. This book builds on the information in Amsco’s Science: Grade 6, and Amsco’s Science: Grade 7. (Turn up the volume and watch our YouTube ad!)
The books in the series correlate 100% to the National Standards for middle school science, the NYS Middle School Core Curriculum for Grades 5–8, and the new Middle School Scope and Sequence for NYC. Each grade covers topics in life, Earth, and physical science. And at each grade level, a unique feature helps students make real-world connections to science. In the grade 6 textbook, the Career Planning section explores science-related careers. Grade 7's Science in Everyday Life feature shows students how science affects their lives. Grade 8 has Science Headline News, which zooms in on current events in science.
At each grade level, the Chapters are divided into Lessons as a planning aid for teachers. Lessons include Skill Activities, Web resources, and little-known science facts to spur student interest. Review sections contain questions of varying levels of difficulty to address the needs of all students. Extended-response questions challenge students to think, analyze, and write.
To order any or all books in the series, visit http://www.amscopub.com/ and click Online Purchasing and then General Science.
If you aren’t a science teacher, you may be thinking that I’m weird, not water. Some people may agree with you, because, after all, I do enjoy chemistry and physics as well as knitting and crocheting. However, in this instance I’m correct. The compounds formed by hydrogen and the Group 16 elements of the Periodic Table of the Elements are not alike. The Group 16 elements are oxygen, sulfur, selenium, tellurium, and polonium. You know that water (H2O) is a liquid at room temperature; its boiling point is 100°C (212°F). At a liquid’s boiling point, the vapor pressure of the liquid is equal to the external pressure. Hydrogen sulfide is a gas at room temperature, as is hydrogen selenide (H2Se). If you graph the boiling points of the hydrogen compounds of these elements, you will find that except for water, the boiling points of these compounds are 0°C (32°F) or lower.
What causes this, you may ask? One answer is hydrogen bonding. Hydrogen bonds form between molecules and hold them to each other. It is a little like cheating. The hydrogen on one water molecule is attracted to the oxygen of another water molecule. When molecules in a liquid “stick together” like this, it takes more energy to separate them and turn them into a vapor. Therefore the boiling point is higher than expected.
Most solids are more dense than their liquid form. Here, water is weird again. We all know that ice floats. Ice is the solid form of water. This means that the solid form of water is less dense than its liquid form. This is very fortunate for us. If ice were more dense than water, it would sink in lakes and ponds, killing anything that had taken refuge from the cold at the bottom. Ice acts as an insulator (slows heat loss), keeping the temperature of the water below it higher than the freezing point.
The Periodic Table: elements with style created by Basher, written by Adrian Dingle, Kingfisher; 2007
What a fresh and original look at the periodic table! The book is compact in size, and gives a brief synopsis, including most the data from the periodic table such as the symbol, atomic number and weight, its standard state, color and classification.
The book is organized by periodic table group, the graphic at the top of the page shows each element's location on the table. The elements introduce themselves with a sense of humor and share facts about their appearance and uses.
Zinc, symbol Zn, says, "Here to protect and serve, I'm more useful than you'd zinc! I'm a very sociable element that's always happy to mix in with other metals."
The illustrations that represent each element make the book. Silicon is a computer chip/centipede while Aluminum is a stylized airplane. They evoke Japanese anime characters and the poster of the periodic table bound into the back of the book remids me of the Pokemon poster that used to hang in my entling's bedroom. I found the drawings utterly compelling.
The book invites casual reading as well as cover to cover absorption.
The DK biography series “A Photographic Story of a Life” picks very well documented subjects. In doing the research for Marie Curie, published in August, I must have brought home at least twenty biographies on her for both children and adults. My problem: What on earth can I bring to the party that that will set my book apart from all the others (aside from the compact and jazzy format set by the publisher)? The answer: me as author.
You see, I have an agenda. I want to get kids interested in science. Marie Curie’s work is intimately connected with the work of other scientists during the twenty-or-so years when chemistry and physics came together and culminated in modern atomic theory—a model of the atom that explained the behavior of gases, chemical reactions, electricity, light, changes of state of matter, radioactivity, the periodic table—in short just about every bit of data that had been accumulating over the previous 200 years in the disciplines of chemistry and physics. A bio of Marie Curie gave me the opportunity to tell a part of that story through the life of an interesting female scientist. For me, it is one fascinating tale.
I also have a bit of biography myself. I know from having been around for a while that there are themes and threads in the life of any multi-faceted human being. Telling a life story by sticking to chronology can make a reader’s eyes glaze over. But telling how a thread develops can be an interesting narrative in itself. Marie was a wife, a mother, a daughter, a patriot of Poland, an expatriot living in France, and the other woman in a sex scandal in addition to be a driven scientist. It was fun to weave in all these threads to the big ideas of the scientific revolution she was a part of. She was a woman in a man’s world and I know what that feels like from some of my experiences, such as being the only female in a pre-med Columbia College organic chemistry course or speaking at the Fermi Lab.
As a children’s book author yet another discipline is imposed on the telling of a story. I am terrified of boring the reader. Most people’s lives don’t unfold like a well-crafted drama. Yet, the demands of today’s entertainment-saturated readers means that I could lose my reader after any sentence. That awareness has been conditioned in me for many years. Above all, it is imperative for those of us who write nonfiction to write a good read.
I think it is the job of a biographer to find points of connectedness with the subject. I found many with Marie Curie as I did with my first DK bio on Harry Houdini. These people were successful and worthy of our admiration because they, too, had agendas that gave their lives purpose and meaning. My life and my biographies have both been enhanced by finding ways for their agendas to fit in with mine.
Ilove fireworks, but only when they are set off by professionals, probably because my maternal grandfather was deaf in one ear because he was too close to a friend’s firecracker when it exploded. I really enjoyed watching the Macy’s Fireworks display on July 4th this year. The explosions came in so many different shapes; some reminded me of far-off galaxies. Then there were the happy faces and, during “Rollin’ on the River,” there were dice. The fireworks also came in many different colors: red, green, blue, lavender, white, and silver. The colors got the chemist in me thinking about how the pyrotechnicians make all those beautiful colors burst in the sky. I knew that it has to do with chemistry.
Fireworks produce three types of energy: sound, heat, and light. The loud booms are the result of the rapid release of energy into the air. This causes the air to expand faster than the speed of sound, producing a shock wave, a sonic boom. You see the aerial display before you hear the boom of the explosion because light travels about a million times faster than sound. That is just like seeing lightning before you hear the thunder.
If you took high school chemistry, you probably remember performing flame tests. You dipped a platinum or Nichrome wire loop into a salt solution, then held the loop in the hottest part of a Bunsen burner flame. Different metallic elements gave the flame a different color. For example, sodium produced a yellow flame and potassium a violet flame. The same principle applies to fireworks.
Listed below, taken from a table at the Chemical of the Week website, are the different elements used to make up fireworks. The colors you see exploding in the sky are produced by the elements with the characteristic emissions listed.
Red: strontium salts, lithium saltslithium carbonate, Li2CO3 = red strontium carbonate, SrCO3 = bright red Orange: calcium saltscalcium chloride, CaCl2
I bet you didn’t know that chemists even had a holiday. Well, a chemist’s favorite holiday is Mole Day! When, you may ask, is Mole Day? Today is Mole Day. It is celebrated annually during National Chemistry Week from 6:02 a.m. to 6:02 p.m. on October 23. Your next question might be: Why are chemists interested in the fuzzy animals called moles? Well, except for those chemists who have a problem with moles in their lawns, most of us don’t give a hoot about moles. However, we do care about the chemical quantity the mole.
A mole is a unit similar to a dozen, which means 12 of anything. A mole is Avogadro’s number of anything. Mole Day commemorates Avogadro's number (6.02 × 1023), which is a basic measuring unit in chemistry. Mole Day was created as a way to foster interest in chemistry. Teachers can find Mole Day cards and mole-related jokes and definitions that can be used to liven up their lessons.
My sons and I celebrate Mole Day every year. Ed has gotten me Mole Day cakes and cupcakes. When he asks the person in the bakery to write Happy Mole Day on the cake or cupcakes, he usually gets a quizzical look. However, last year the young woman at the Butter Cooky Bakery knew just what he was talking about. She remembered it from when she took chemistry.
Click on the link to listen to the Mole Day song and have a Happy Mole Day!
Thorium, element 90 on the Periodic Table of the Elements, is a lustrous, silvery-white metal that is only slightly radioactive. In fact, the mantle in the portable gas lamps that people use on camping trips contains thorium. The element was named for Thor, the Norse god of thunder. Thorium is a member of the actinides, which are found in the bottom row of the Periodic Table. The actinides, which include uranium, release particles (including neutrons) from the nucleus and decay into more stable elements. These neutrons can hit nearby atoms, causing them to split and release even more neutrons. This results in a chain reaction that releases energy. If the chain reaction is uncontrolled, the result is a nuclear explosion. By controlling the chain reaction, these elements can be used to generate power.
Thorium may be the element that solves the problems of generating energy using nuclear fuel. After thorium has been used to generate power, it leaves behind only a tiny amount of waste. In contrast to wastes generated by uranium-fueled plants, which must be stored for hundreds of thousands of years, the waste from thorium-fueled plants would need to be stored only for a few hundred years. Thorium is plentiful and virtually inexhaustible and does not require costly processing. In theory, it acts as a breeder, creating enough new fuel as it breaks down to sustain a high-temperature chain reaction indefinitely.
Thorium would used in a new type of reactor, a liquid fluoride thorium reactor, that would have no risk of meltdown. Alvin Weinberg, former director of the Oak Ridge National Lab, and his team built a similar reactor in 1965. In this working reactor, the byproducts of thorium were suspended in a molten salt bath.
Why haven’t uranium reactors been replaced by thorium reactors? Critics point out that because the reaction is sustained for a long time, the fuel needs special containers that are very durable and can withstand the corrosive molten salts. In addition, replacing the reactors already in service would be extremely expensive.
There is a compromise solution. Uranium reactors can be converted to seed-and-blanket reactors that use thorium oxide and uranium oxide rods. The core of the reactor is a seed of enriched uranium rods surrounded by a blanket of thorium oxide/uranium oxide rods. The result is a safer, longer-lived reaction than uranium rods alone. In addition, it produces less waste and the waste cannot be used for nuclear weapons.
It is a start. I hope they find a way soon to solve the technical problems of the liquid fluoride thorium reactor and replace all the uranium reactors.