A Child’s Curiosity

Posted on May 19, 2014 by Danae Dodge

“What is gravity?” asks my then four year old nephew to his family.
Quite an inspirational question from a four year old! But then again, at the time they were all watching the highly acclaimed Cosmos; the science documentary hosted by Neil deGrasse Tyson. A child’s curiosity clearly knows no bounds when it comes to the world around them, and I am astounded by the equally captivating questions his brother asks me (“What does e in math[s] mean?”)
It is sad that in later years children eventually lose their interest in science. In 2008, The Telegraph published a report with statistics that showed some children were losing their interest between primary and secondary school (42% of 9 year olds were interested in science, but this drops to 38% of 12 year olds and 35% of 14 year olds). In 2013 Ofsted reported an assessment of science education and recommendations based on a survey [Maintaining curiosity: a survey into science education in schools] conducted between 2010 -2013. CaSE in London responded positively to this report and has called for the UK Government to heed these recommendations.

I had the chance to observe such inspirational curiosity during my Easter holidays when I visited my cousin and her children (hereafter referred to as my niece and nephews) in Boston, centre of scientific excellence. It really doesn’t get any better than that! One of the things I was particularly looking forward to was extracting DNA from strawberries with them. I had of course previously done this with Science Brainwaves at a school outreach event in 2011. Just telling my 11 year old niece and 9 year old nephew about this got them really excited. When I told them their dining table needed to be cleaned, my nephew (who prefers to kick a football around the house much to his parents’ disapproval) was so eager that he could not clean the table fast enough! I complemented this little experiment with a brief 101 on DNA and PCR (polymerase chain reaction, which copies DNA). When I interviewed them later about it, they told me they loved it and would gladly do it again. Score 1 for science! If doing practical experiments benefits children so much, then it certainly makes the removal of practical work for A’ Level exams by Ofqual in the UK dubious. Naturally, this move has been criticised and on the 12th May 2014, a hearing was hosted by the Commons Select Committee to discuss this proposal.

I also had the opportunity to visit some of the scientific attractions of Boston with the kids; the New England Aquarium and the Museum of Science. I found that the trip to the aquarium was definitely worthwhile. My nephew had his own epiphany linking the ecology of sharks and their prey to the food web, as he dictated later in the evening. I was amazed and a little scared when I had the chance to touch stingrays and a baby shark in the giant ‘touch-tank’. But I wasn’t the only one in seventh heaven. It was interesting to find out that my niece actually wants to be marine biologist. Score 2 for science. I asked my 9 year old nephew what he wanted to do and he replied with a list of potential careers: archaeologist, cosmologist or footballer. I was completely honest with him when I said that he might make more money becoming a footballer, there probably won’t be very much opportunities in archaeology, but that cosmology might be more fulfilling. He didn’t seem too upset or waylaid by this. I neglected to ask the youngest, as at the time he was 4 years old and most of his ambitions included chocolate and tickling. I will ask him another time.

When it comes to their parents encouraging them into science, my cousin and her husband do not hold back! Amazed by my nephew’s questions, the family is now subscribed to the Scientific American and together they all sit down to watch Cosmos. This documentary, playing on Fox and National Geographic, follows on from the Carl Sagan version which played in 1980. I watched the second [Some of the Things That Molecules Do] and fourth [A Sky Full of Ghosts] episodes, glad that the second episode provided a neat and tidy introduction to genetics and evolution, the ideal precursor to extracting DNA from strawberries. I was really astounded at how the show pitched itself perfectly to both adults and children. The parents and all three kids were glued to the screen, and I found the balance between explanation and visuals in complete harmony. But of course, a documentary like this does not go unnoticed by the Creationists in the USA, especially when evolution is involved. In an article in the Huffington Post, the show was criticised by Creationists for not given its due time on Creationism. I asked my niece and nephew what they thought and they make the same claims as any scientist would make: Why give inaccurate information to the public, especially when there is evidence to back up what we already know? Score 3 for science.

For the final flourish in this scientific journey with my niece and nephew I tell them I write a monthly blog for Science Brainwaves. So I asked them to read Resurrection! Bringing species back from the dead, and get their thoughts and feedback. They both would like to see the sabre tooth cat brought back (clearly indicating they have not seen Jurassic Park). My niece is for bringing back species from the dead as she thinks it will make great study material. My nephew on the other hand is a lot more cautious. I don’t think I can score this as either for or against science, but I’m definitely happy to see this younger generation at least considering the ethical options. Either way, the final score is 3 for science, I’m still the Cool Fun Aunt and now I can happily watch and nurture their scientific ambitions to reality.

Doing DNA extraction with my niece and nephew

The touch tank at the New England Aquarium

Interbreeding humans: The Sassy Palaeolithic Action

Posted on March 14, 2014 by Danae Dodge

Are you confused about the different types of humans that got it on with each other?
If you are, then in this blog entry, I provide a summary factsheet style of the pairs of hominids that interbred with each other, with evidence for and against it, and the current conclusion. All dates are expressed as years before present, and be aware that in the field of ancient DNA, human contamination is always an issue that can potentially confound the results.

Hominid Action Pair #1:     Neanderthals     +        Humans: Non-Africans
Home-turf:    Europe/Asia                       Global
Lived from:                        400,000 – 30,000             200,000- present
When and where:                     47,000-65,000 Middle East
Evidence for getting it on: If the different colours represent different genetic make-up, then the answer to the question “Where did the modern humans get their genes from?” can only be “from mating with Neanderthals”.

Evidence against getting it on: This model clearly produces the same pattern but without mating.

Current status: The literature arguing against interbreeding has been focused on the pitfalls of the method used. Nevertheless, new methods are now confirming that Neanderthals and humans were up in a tree K.I.S.S.I.N.G. Now, we are starting to identify what genes we got from them.

Hominid Action Pair #2:         Denisovans      +      Humans: Asians/ Oceanians
Home-turf:                       Siberia (Tropics?)                       Oceania
Lived from:                        ? – ~50,000                       200,000- present
When and where:                      S.E Asia and prior to 44,000
Evidence for getting it on: It’s the same case as the evidence for mating between Neanderthals and humans, except here the genes that went into the ancestral populations of the Aboriginal Australians, Near Oceanians, Polynesians, Fijians, East Indonesians, and Philippine Mamanwas and Manobos can only have come from the Denisovans.
Evidence against getting it on: While models are presented in the literature for discussion, they have been argued against. The consequence of which is that the results are described as a best fit to the data.
Current Status: We know that the action took place BUT we don’t know enough about the Denisovans. We only have a tooth and small finger bone from a Siberian cave. Watch this space!

Hominid Action Pair #3:              Denisovans       +         Homo erectus?
Home-turf:                              Siberia (Tropics?)        Africa, China, Indonesia
Lived from:                                 ? – ~50,000               1.9 million years- 150,000
When and where: ? and Asia?
Evidence for getting it on: The Denisovan tooth has some features that you can find in some of the older Homo species, and the DNA appears to also look quite archaic. Homo erectus was widespread across Asia, so it does seem likely that the two hominids crossed paths.
Evidence against getting it on: At the minute, there isn’t any. This model was proposed as the most likely scenario to a result that arose from another study.
Current Status: As already said before, we don’t know that much about the Denisovans. There are still a lot of gaps making this a hypothesis.

Hominid Action Pair #4:             Neanderthals        +       Denisovans
Home-turf:    Europe/Asia              Siberia (Tropics?)
Lived from:                                400,000 – 30,000              ? – ~50,000
When and where:                                    ? and Europe/Asia?
Evidence for getting it on: Evidence against getting it on: Not presented.
Current Status: This has just recently been published, and the amount of DNA material from the Neanderthals into the Denisovans is calculated to have been very small. More analyses will have to be done.

*********************************

Summary
Here is a final tree summarising the relationships between the hominids, and the arrows indicate where interbreeding took place. Adapted from Prufer et al 2014.

While I used a lot of literature to create the above summary, if you are looking for more information then I recommend Veeramah and Hammer 2014, Nature Reviews Genetics 15, 149-162 as it provides an up to date informative review while also including relevant references.

Resurrection! Bringing extinct species back from the dead

Posted on February 14, 2014 by Danae Dodge

My best friend has nightmares about dinosaurs; T. rexes chasing and searching for her as she hides behind furniture. I don’t blame her. Courtesy of Jurassic Park, I’m sure there are plenty of others who have had similar nightmares. During my PhD, I once had a nightmare that Neanderthals were back and trying to take over Europe. But is it really possible to bring back species from the dead?

At first glance, it seems to be more difficult than the movies give credit for. In 2009, the New Scientist published an article outlining the method for any Dr Moreau wannabes, but also why the technology is not available for it to work:

1- Obtain a complete and accurate genome

2- Package and assemble this genome into chromosomes

3- Identify a suitable surrogate to provide the egg and to gestate the embryo to full term

But as technology is moving at a face pace the limits of scientific accomplishments are being further tested. Revive and Restore is a project aiming to push the boundaries for resurrecting extinct species. Inspiration for this project came when the last passenger pigeon (a species hunted to extinction for its meat) named Martha died in Cincinnati Zoo in 1914. Several species have since been chosen as candidates to be resurrected, including a range of birds, the quagga, the Easter Island palm and several Pleistocene mammals. The first meeting held on the 8 February 2012 brought together conservation biologists and geneticists to assess the feasibility of resurrection. Since then the project has established a list of criteria to examine the suitability of each candidate species, e.g. how will bringing back the species answer scientific questions, is it possible to re-wild a species and, if selecting a species further back in time, is there enough preserved DNA. Sure enough in 2013 an article What If Extinction Is Not Forever? appeared in Science discussing the risks versus the benefits. The objections fell into five categories: animal welfare, health, environment, political and moral, and the benefits included: scientific knowledge, technological advancement, environmental benefits, justice and the “cool” aspect of it.

One of the reasons why the passenger pigeon was selected is because there are plenty of samples that are young enough to obtain good quality DNA. The key issue therefore lies in the survivability of ancient DNA sequences. The potential rests firstly in obtaining increasingly older DNA sequences and secondly, ensuring that the genome is of high quality. The oldest DNA sequence obtained to date is the 700,000 year old horse genome from Canada, a far cry from what was once an hypothesised maximum of 100,000 years old (Shapiro and Hofreiter, 2014). Sequencing technologies have also drastically increased genome coverage (how many times a gene is “read” a bit like each time you re-read a book you pick up on more information and with better accuracy). The Denisovan genome, for instance, before the use of the new sequencing technology enabled a coverage of 1.9 fold, which increased dramatically to 30 fold once the new techniques were applied. Nevertheless even with the new technology to analyse fragmented DNA, Shapiro and Hofreiter (2014, p. 1236573-2) state “it may not be possible to sequence any eukaryotic palaeogenome truly to completion”- a sad case indeed for the 11 year old boy who once asked me at a Science Brainwaves workshop “can we bring monsters back?” Assuming he meant dinosaurs and without getting into the logistics with him, I gave him the theoretical but not entirely true response of ‘yes’. He then exclaimed “COOL” really loudly and wondered off. To be honest, I didn’t really want to break his heart, and I may just have inspired him to become a scientist! A similar question was posed (in a considerably much more professional manner) at the Royal Society meeting in London Ancient DNA: the first three decades in November 2013. Towards the end of the talk The Future of aDNA by Professor Michael Hofreiter, a colleague from UCL asked “can we reconstitute from ancient DNA (putting aside the technical details) a viable sequence to create a viable organism?” The answer was a resounding no. When it came to resurrecting dinosaurs, Professor Hofreiter quite clearly stated that the field of ancient DNA will never be able to go that far back in time. With an added flourish came the phrase “don’t waste your time or money!”

So should we be worried about dinosaurs chasing us, or Neanderthals taking over? With the advancement of technology opening up the possibility of resurrection, it is only those that have not been extinct for very long that could be resurrected, such as the dodo or the passenger pigeon. The debate on this however continues: It is through this approach that together scientists, policy-makers and the public can work together to ensure that this new science is used in a mature and sensible way. As for my best friend, she is relieved and hasn’t had a dinosaur nightmare since.

Jurassic Park, copyright IMDB Universal Pictures 2012

Neolithic Revolution in the air!

Posted on December 2, 2013 by Danae Dodge

THE NEOLITHIC REVOLUTION WAS A KEY MOMENT IN THE PREHISTORY OF HUMANS. It sparked civilisation as we know it- settlements were established, crops were grown and animals were domesticated transforming the economy of subsistence globally. Beginning in the Levant (Near East) around 12,000 years ago, the Neolithic Revolution spread into Europe 8000 years ago and lasted up until 4000 years ago when the Bronze Age began.

The major question is how did this revolution spread? Did the indigenous hunter gatherers adopt farming solely though cultural transmission? Or did the farmers pass on their practices alongside their genes? These two models (see diagram) – culturally diffused model (CDM) and demic diffused model (DDM) – originally seen as two polar opposites as mechanisms of the spread, have been debated throughout the 20^th century. By identifying the proportion of Mesolithic/ hunter-gatherer and Neolithic/ farmer genes within the current gene pool (see diagram), the correct model could be identified.

Classical genetic markers in present day populations (such as blood groups) appear to lend support to the DDM revealing a genetic cline from the Near East towards the West. But modern genetic markers can reflect population processes that have taken place both before and after the Neolithic spread. Instead ancient DNA (aDNA) provides a unique window of opportunity to look back into the past. Ancient DNA studies do come fraught with difficulties. Over time DNA degrades and fragments into short molecules. Usually this means any contaminating modern DNA is favourably extracted and analysed instead. Nevertheless strict and rigorous protocols exist to minimise contamination and new technology has been optimised for aDNA extraction.

The archaeological record has shown that as farmers migrated across Europe, two different routes were taken as indicated by distinct ceramic styles. One route was through Central Europe, from Hungary to Slovakia, Ukraine and through to Paris, as shown by the Linearbandkeramik (LBK) and Alföldi Vonaldiszes Kerámia (AVK) pottery styles. The other route represented with Impressed Ware/Cardial culture was along the Mediterranean coast. aDNA studies have been conducted on samples from these different sites and cultures, and the picture that emerges is one more complex than just picking one model over the other. It certainly appears that the two routes have their own model: while the Central Europe/ LBK route shows little to no genetic continuity between the Mesolithic hunter-gatherers and the Neolithic farmers, the Mediterranean route tends towards genetic continuity and therefore a level of gene flow between the two populations, a pattern which even seems to lead up into Sweden.

But this most certainly is not the end of the story. For one thing, the genetic studies carried out were analysing the mitochondrial DNA (mtDNA), which is inherited solely down the female line (men inherit their mothers’ mitochondrial DNA but will not pass it on). In one study, it was found that of Spainish Neolithic samples while the mtDNA belonged to hunter gatherer groups from the Palaeolithic, the Y chromosome was shown to be from the Neolithic Near East. This does seem to suggest that the role of men and women during the advance of the Neolithic differed to some extent. Additionally, it also appears that the change to farming practices did not happen as rapidly as expected, and was not as clear cut. In two recent papers (with a particular focus on Germany), it was found that hunter gatherers and farmers lived alongside each other for about 2000 years and, interestingly while the Mesolithic hunter gatherers and the Neolithic farmers had their own distinctive gene pools, at some point in the Neolithic there were intermediary groups with shared ancestry and lifestyle undoubtedly reflecting the transition that was taking place.

There is a level of difficulty when studying the past; we cannot always state processes or cause and effects with a perfect degree of certainty, but we can say what the evidence appears to suggest, and in this case it appears to suggest a high a degree of complexity as the Neolithic Revolution took hold. There is never just any one specific model that can answer our questions, and there will always be other lines of evidence to explore. To answer the original question how the Neolithic Revolution spread cannot be placated with just one simple answer. It is never that easy. But as aDNA analyses show, we can still get one step closer to that very complicated answer.

More information:

Bollongino et al 2013 Science 342 (6157) 479-481

Brandt et al 2013 Science 342 (6155) 257-261

Gamba et al 2011 Molecular Ecology 21 (1) 45-56

Haak et al 2005 Science 310 (5750) 1016-1018

Lacan et al 2011 PNAS 108 (45) 18255–18259

Pinhasi et al 2012 Trends in Genetics 28 (10) 496-505

Skoglund et al 2012 Science 336 (6080) 466-469

Reproduction Revamp: Stick Insects and Going It Alone.

Posted on November 21, 2013 by Marni Brennan

125227306.pX5ldchw

Timema cristinae: making a lack of a love life cool.

Love can be tough. If you wish awkward dates and trawling through match.com were a thing of the past, you could take a leaf out of this stick insect’s book. Tanja Schwander (University of Lausanne) studies how Timema stick insects are changing the dating game. Rather than reproducing with a partner, female Timema have developed the ability to produce offspring individually. There could be a number of causes for this bizarre transition from sexual to non-sexual offspring production, so read on for a how-to guide in ditching dating.

Conversion to non-sexual reproduction may occur genetically. When female Timema are prevented from mating, some eggs that haven’t been fertilised by sperm hatch and develop. Could this virgin birth scenario, reminiscent of biblical times, replace sexual reproduction in Timema? Or are virgin births merely a strategy to ensure female stick insects can carry on their line when opportunities to mate are thin on the ground?

Alternatively, a type of bacterial infection may stimulate non-sexual reproduction. Infecting bacteria are only transmitted through the female sex cell, the egg, and so males slow the spread of the bacteria. In light of this, the bacteria devised a cunning strategy to eliminate males: inducing a kind of non-sexual reproduction that produces only female offspring. Could bacterial infection be the instigator of non-sexual reproduction?

Schwander’s studies of genetic data reveal the virgin birth scenario cannot explain the change in Timema reproduction. Conversion to non-sexual reproduction may occur genetically, but not via virgin births. To determine if bacterial infection causes the stick insect’s lack of libido, Schwander cured the infection. This restored sexual reproduction and production of male offspring, proving bacterial infection can result in non-sexual reproduction. Watch this space; could Boots’ next bestseller be bacteria to eliminate human males?

Designer Babies- What’s It All About?

Posted on October 30, 2013 by Emily Sims

Throughout the social and scientific worlds, there is controversy surrounding the potential to genetically modify embryos to create ‘designer babies’. These are embryos that have been screened for genetic diseases, and will therefore only contain selected desired qualities chosen by the parents. However, there are many stories in the media which exaggerate and distort the facts- and this can even be seen in the term ‘designer babies’ itself. It is important to think about the likelihood and implications of this idea, plus to outline what actually gave rise to this concept.

We could suggest that the idea of genetically engineered embryos or the ideas that led to this originated in 1978 and the first in-vitro fertilisation (IVF) treatment. The procedure gave and still gives hundreds of infertile couples a chance to have a child by transferring an egg fertilised in a laboratory into the mothers uterus. It subsequently led to a procedure known as preimplantation genetic diagnosis (PGD). This is a technique used on embryos to profile their genome- it is a form of genetic profiling and embryo screening and is a more technical and accurate way of regarding ‘designer babies’. In terms of health benefits, using PGD means embryos can be screened outside the womb. Embryos can be selected that only carry normal and healthy genes, and are therefore free from genetic abnormalities. Whilst this technique is currently popular, PGD could in the future be used to select any desired specified trait of a child, such as eye colour, intelligence, and athleticism; be used to select embryos to be without a genetic disorder, to increase successful pregnancies, to match a sibling in order to be a donor, for sex selection and therefore be used to design your own baby. Selecting the gender of a child is already possible due to the fact only the X or Y chromosome needs to be identified, but other traits are more difficult due to the amount of genetic material required. Recent breakthroughs have meant that every single chromosome in an embryo can be scanned for genes involved in anything from Down’s Syndrome to lactose intolerance using a single microchip, but how advanced is this and what are the ethics behind this?

There are a large array of ethical, social and scientific concerns over the concept of creating a ‘perfect’ child. Some people worry that in the future there will be an imbalance between genders in the general population especially in societies that favor boys over girls, such as China. Also, a key issue suggested is that there is an element of eugenics to this idea- PGD will mean that people with ‘unattractive’ qualities will be lessened and potentially society may discriminate against those who have not been treated. If we look at this from a more extreme perspective, it could be suggested that we may end up with a race of ‘super-humans’ and a divide between those who have been treated and those who haven’t. Also, this selection of genotypes suggests a potential deleterious effect on the human gene pool, meaning less genetic variation. Whilst at first this may seem positive due to the fact you could eliminate genetic disorders such as hemophilia A before it becomes prevalent in the body, it is also likely that new diseases may evolve and accidentally be introduced into the human race. Due to the decreased gene pool, only partial evolution would be able to occur and therefore we will be more susceptible to new diseases having a dramatic effect. It is clear from this evidence that regulations must be put in place and strictly enforced before any new advances are made.

So, how close are we to being able to ‘customise’ our children?
In terms of altering genes already present in the embryo, we are already well on our way to refining this technology. Scientists have been altering animal genes for years, and germline therapy is already being used on animals. Germline gene therapy is now being closely linked and developed with PGD- and it could soon be used to change human genetics. Our germline cells are our sex cells (egg and sperm), and using this branch of gene therapy essentially involves manipulating and adding new genes to the cells. The clear possibility from this in terms of PGD is that any trait can be added to an embryo to create a designer baby. This may involve adding a gene to stop a genetic disorder being expressed in a baby’s phenotype by fixing them as they are noticed in PGD, but it could also mean that only certain people will be able to advance in society.

On he other hand however, before these ‘more advanced’ humans are created we need to learn more about the genetic code. The basis of all genetic technologies lies in the human genome, and whilst PGD advances are ever-increasing, at present we can only use this technique to look at one or two genes at a time. Therefore, we cannot use it to alter the genes in embryos, and this would logically lead us to think about gene therapy, but the current lack of technology and the strict regulations regarding experimenting with germline gene therapy makes it unlikely that anyone will be able to create a completely designer baby in the near future.

Designing our babies is a reality that government bodies and various organizations are beginning to accept and address fully, and society’s view of the moral implications behind PGD and gene therapy being a key factor in determining how far this concept can advance; there will be increasingly new debates and controversy over the acceptable applications of gene technologies in humans and human embryos.

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.

_________________________________________________________________________________________________________

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.