Biotech for all – taking science back to it’s roots?

Posted on May 18, 2013 by LHeywood

This morning I came across a very interesting TED talk by Ellen Jorgensen entitled “Biohacking — you can do it, too” (http://on.ted.com/gaqM). The basic premise is to make biotech accessible to all, by setting up community labs, where anyone can learn to genetically engineer an organism, or sequence a genome. This might seem like a very risky venture from an ethical point of view, but actually she makes a good argument for the project being at least as ethically sound than your average lab. With the worldwide community of ‘biohackers’ having agreed not only to abide by all local laws and regulations, but drawing up its own code of ethics.

So what potential does this movement have as a whole? One thing it’s unlikely to lead to is bioterrorism, an idea that the media like to infer when they report on the project. The biohacker labs don’t have access to pathogens, and it’s very difficult to make a harmless microbe into a malicious one without access to at least the protein coding DNA of a pathogen. Unfortunately, the example she gives of what biohacking *has* done is rather frivolous, with a story of how a German man identified the dog that had been fouling in his street by DNA testing. However, she does give other examples of how the labs could be used, from discovering your ancestry to creating a yeast biosensor. This rings of another biotech project called iGem (igem.org), where teams of undergraduate students work over the summer to create some sort of functional biotech (sensors are a popular option) from a list of ‘biological parts’.

The Cambridge 2010 iGem team made a range of colours of bioluminescent (glowing!) E.coli as part of their project.

My view is that Jorgensen’s biohacker project might actually have some potential to do great things. Professional scientists in the present day do important work, but are often limited by bureaucracy and funding issues – making it very difficult to do science for the sake of science. Every grant proposal has to have a clear benefit for humanity, or in the private sector for the company’s wallet, which isn’t really how science works. The scientists of times gone by were often rich and curious people, who made discoveries by tinkering and questioning the world around them, and even if they did have a particular aim in mind they weren’t constricted to that by the agendas of companies and funding bodies. Biohacking seems to bring the best of both worlds, a space with safety regulations and a moral code that allows anyone to do science for whatever off-the-wall or seemingly inconsequential project that takes their fancy – taking science back to the age of freedom and curiosity.

A matter of inheritance

Posted on January 20, 2013 by Rob Hoskin

Image courtesy of ‘Digital Dreams’ / FreeDigitalPhotos.net

The age-old ‘nature-nurture’ debate revolves around understanding to what extent various traits within a population are determined by biological or environmental factors. In this context ‘traits’ can include not only aspects of personality, but also physical differences (e.g. eye colour) and differences in the vulnerability to disease. Investigating the nature-nurture question is important because it can help us appreciate the extent to which biological and social interventions can affect things like disease vulnerabilities, and other traits that significantly affect life outcomes (e.g. intelligence). The ‘nurture’ part of this topic can be dealt with to some extent by research in disciplines such as Sociology and Psychology. In contrast genetic research is crucial to understanding the ‘nature’ part of the equation. Genetics also has relevance for the ‘nurture’ part of the debate because environmental factors such as stress and nutrition affect how genes perform their function (gene expression). Indeed genetic and environmental factors can interact in more complex ways; certain genetic traits can alter the probability of an organism experiencing certain environmental factors. For example a genetic trait towards a ‘sweet tooth’ is likely to increase the chances of the organism experiencing a high-sugar diet!

Given the importance of genetic information to understanding how organisms differ, I would argue that a basic knowledge of Genetics is essential for anyone interested in ‘life sciences’. This is true whether your interest is largely medical, psychological or social. Unfortunately if, like me, you skipped A-Level Biology for something more exciting (or A-Level Physics in my case!) you might Genetics at bit of mystery.

Some basic genetics

Genetic information is encoded in DNA (Deoxyribonucleic acid). Sections of DNA that perform specific, separable functions are called Genes. Genes are the units of genetic information that can be inherited from generation to generation. Most Genes are arranged on long stretches of DNA called chromosomes, although a small proportion of genes are transmitted via cell mitochondria instead. Most organisms inherit 2 sets of chromosomes, one from each parent. Different genes perform different functions, mostly involving the creation of particular chemicals, often proteins, which influence how the organism develops. All cells in the body contain the DNA for all genes, however only a subset of genes will be ‘expressed’ (i.e. perform their function) in each cell. This variation in gene expression between cells allows the fixed (albeit very large) number of genes to generate a vast number of different chemicals. This in turn allows organisms to vary widely in form while still sharing very similar genetic information (thus explaining how it can be that we share 98% of our DNA with monkeys, and 50% with bananas!).

The complete set of genetic information an individual has is called their ‘genotype’. The genotype varies between all individuals (apart from identical twins) and thus defines the biological differences between us. In contrast the ‘phenotype’ is the complete set of observable properties that can be assigned to an organism. Genetics tries to understand the relationship between the genotype and a particular individual phenotype (trait). For example how does the genetic information contained in our DNA (genotype) influence our eye colour (phenotype)? As already mentioned environmental factors play a significant role in altering the phenotype produced by a particular genotype. Explicitly the phenotype is the result of the expression of the genotype in a particular environment.

Heritability

Roughly speaking, heritability is the influence that a person’s genetic inheritance has on their phenotype. More officially it is the proportion of the total variance in a trait within a population that can be attributable to genetic effects. It tells you how much of the variation between individuals can be attributed to genetic differences. Note that this is not the same as saying that 60% of an individual’s trait is determined by genetic information. In narrow-sense heritability (the most common form used), what counts as ‘genetic effects’ is only that which is directly determined from the genetic information past on by the parents. This ignores variations caused by the interaction between different genes, and between genes and the environment. This is the most popular usage of heritability in science because it is far more predictive of breeding outcomes, and therefore tells us more about nature part of the ‘nature-nurture’ question, than the alternative (broad-sense) conceptualisation of heritability.

Uses and abuses

Genetic research can provide crucial information in the fight against certain diseases. Identifying genes that are predictive of various illnesses allow us to identify individuals who are vulnerable to a disease. This then allows preventive measures to be implemented to counter the possible appearance of the disease. Furthermore once the genes that contribute to a disease are known, knowledge as to how those genes express will help reveal the cellular mechanisms behind the disease. This improves our understanding of how the disease progresses and operates, and therefore helps with identifying treatment opportunities. In reality of course Genetics is rarely this simple. Many conditions that have a genetic basis (i.e. that show a significant level of heritability) appear to be influenced by mutations within a large number of different genes. Indeed in many cases, especially with psychiatric disorders, it may be that conditions we treat as one unitary disorder are in fact a multitude of different genetic disorders that have very similar phenotypes. Nevertheless, despite these problems genetic research is helping to uncover the biological basis of many illnesses.

One problem with Genetics, and heritability in particular, is that of interpretation. There is often a mistaken belief that a high level of heritability signifies that environmental factors have little or no effect on a trait. This misunderstanding springs from an ignorance of the fact that estimates of heritability comes from within a particular population, in a particular environment. If you change the environment (or indeed the population) then the heritability level will change. This is because gene expression is affected by environmental factors and so the influence of genetic information on a trait will always be dependent to some extent on the environment. As an example a recent study showing that intelligence was highly heritable (1) lead to some right-wing commentators using it as ‘proof’ of the intellectual inferiority of certain populations, because of their lower scores on IQ tests. Such an interpretation is then used to argue that policies relating to equal treatment of people are flawed, because some people are ‘naturally’ better. Apart from the debatable logic of the argument itself, the actual interpretation of the genetic finding is flawed because a high heritability of IQ does not suggest that environmental differences have no effect on IQ scores. To illustrate this point consider that the study in question estimated heritability in an exclusive Caucasian sample from countries with universal access to education. If you expanded the sample to include those who did not have access to education it would most likely reduce the estimate of heritability, as you would have increased the influence of environmental factors within the population being studied! Ironically therefore you could argue that only by treating everyone equally would you be able to determine those who are truly stronger on a particular trait! Independent of what your views on equality are, the most important lesson as regards genetics is that you cannot use estimates of heritability, however high, to suggest that differences in the environment have no effect on trait outcomes.

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References

(1) Davies, G. et al (2011) Genome-wide association studies establish that human intelligence is highly heritable and polygenic. Molecular Psychiatry 16, 996-1005. http://www.nature.com/mp/journal/v16/n10/full/mp201185a.html

Although not directly cited, I found the following information useful when creating the post (and when trying to get my head around Genetics!).

Quantitative Genetics: measuring heritability. In Genetics and Human Behaviour: the ethical context. Nuffield Council on Bioethics. 2002. http://www.nuffieldbioethics.org/sites/default/files/files/Genetics%20and%20behaviour%20Chapter%204%20-%20Quantitative%20genetics.pdf

Visscher, P.M., Hill, W.G. & Wray, N.R. (2008) Heritability in the genomics era – concepts and misconceptions. Nature Reviews Genetics, 9 255-266. http://www.ncbi.nlm.nih.gov/pubmed/18319743

Bargmann, C.I. & Gilliam, T.C. (2012) Genes & Behaviour (Kandel, E.R. et al (Eds)). In Principles of Neural Science (Fifth Edition). McGraw-Hill.

Dominant and Recessive Genes In Humans

Posted on June 18, 2011 by admin

As briefly referred to in the previous Genetics blog, for each of our genes we posess two ‘alleles’. One of these alleles in inherited from our father and one from our mother. There can be many different alleles for one gene and it can be completely up to chance, or perhaps luck, what we inherit from our parents. When speaking in general terms about dominant and recessive alleles, we tend to speak about genes as if for each of them there are two different alleles. This is not always, or often, the case, but it sometimes is and makes it much easier to explain this way.

For example, for a particular gene, say the ability to roll your tongue, there is a dominant and a recessive gene. We can call the dominant allele ‘R’ for being able to roll our tongue and the recessive allele ‘r’ for being unable to roll our tongue. Our parents could posess any combination of these alleles: AA, aa or Aa. Then, it is completely down to chance what we inherit from them.

One unexpected example is that the allele for dwarfism in humans is the dominant allele and the allele for normal growth is recessive. This means that if we inherited both of the different alleles for this gene we would show the dwarfism trait.

Below is a table of dominant and recessive traits shown in humans.

Dominant Trait in Humans	Recessive Trait in Humans
A blood type	O blood type
Abundant body hair	Little body hair
Astigmatism	Normal vision
B blood type	O blood type
Baldness (in male)	Not bald
Broad lips	Thin lips
Broad nose	Narrow nose
Dwarfism	Normal growth
Hazel or green eyes	Blue or gray eyes
High blood pressure	Normal blood pressure
Large eyes	Small eyes
Migraine	Normal
Mongolian Fold	No fold in eyes
Nearsightedness	Normal vision
Rh factor (+)	No factor (Rh -)
Second toe longest	First or big toe longest
Short stature	Tall stature
Six fingers	Five fingers normal
Webbed fingers	Normal fingers
Tone deafness	Normal tone hearing
White hair streak	Normal hair coloring

When we are speaking about the inheritance of alleles and the genetic make-up of a person with respect to one gene, we use one of two phrases. The first is homozygous, meaning that the two alleles an individual posesses for one gene are the same i.e. AA or aa. The second is heterozygous, meaning that the two alleles an individual posesses for one gene are different i.e. Aa.

By Robyn Bradbury

Finding out what makes you, you.

Posted on February 11, 2011 by admin

Although Genetics is often seen as just another jigsaw piece making up the wide subject of Biology, it really underlies the whole study.

After all, is the most fundamental question of life not how does the set of chemicals inside us provide our every essence? How are those chemicals changed from simple molecules to everything that makes up a human being?

One thing which makes Genetics so interesting is that not even the best geneticists in the world can fully answer these questions. It is still a science very much in its infancy and early stages of understanding. After all, it was only around sixty years ago that James Watson and Francis Crick made the discovery of the structure of the DNA double helix. What is most fascinating about how these men made their discovery is that they came to their final theory of the double helix without any experiments of their own; they simply brought together other people’s evidence and used it to their advantage to gain their own final answer.

The less molecular side of Genetics which most people have heard something of is that of Gregor Mendel’s pea plant experiments: he performed genetic crosses with the plants, noting parent and offspring characteristics. As far back as 1856, he laid the foundations of what remain the basic principles of Genetics in these modern times. Mendel introduced the theory of recessive and dominant characteristics, without fully understanding what he was proposing.

A gene, in simplified terms, is a stretch of DNA coding for a characteristic in an organism. Allele is the word used when there are two or more different forms of a gene, so there can be different alleles for a particular gene. These different alleles can be classed as recessive or dominant, which basically do as their names suggest i.e. genes come in stronger or weaker forms; dominant being stronger and recessive being weaker. This means that one allele can dominate over the other and if both alleles occur, the so-called dominant allele will be shown. Since we have two copies of every gene, one from our mother and one from our father, any allele combination can occur. Therefore for a gene with two alleles, A (dominant) and a (recessive), there are three different allele couplets which could occur: AA, Aa or aa. This is called the organism’s genotype, the genes contained within its cells. The organism’s genotype produces a particular phenotype, which is the characteristic shown by an organism due to its genotype. For instance, in Mendel’s pea plant experiment, he found that yellow colour is dominant to green colour in the peas – yellow colour could be shown by the allele Y and green colour can be shown by the allele y. This means that in this case, the pea plant can have the genotypes of YY or Yy which will show a yellow phenotype, or yy which will show a green phenotype.

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Category Archives: Genetics