A defence of diversity in science

A particular pianist is remembered for their unique style of play, repertoire of musical pieces, and their distinctive command of the piano. In this sense we are all defined by our own style, methods, and toolkit. As scientists this may not seem so obvious, as we like to think we all employ the same scientific method and unlike a pianist, who may play Chopin with melancholy or rapture, we apply it in more or less the same bog-standard way. This cannot be further from the truth. Some scientists take a more broad approach: focusing on unifying large bodies of knowledge; a few hop between relatively small unrelated problems and fields; many work in a single field for most of their lives. Even in the latter category there are multitudes of scientific styles, methods, and tools. Laser tinkerers, gene creatives, equation eccentrics, software superheroes, and cell culture crews are but a swab of the various kinds of scientists out there. My point is that science can be, and is, done in many different ways.

We judge a pianists work by some arbitrary criteria that defines 'good' music (I don't have a clue what criteria this is). However, in science the threshold criteria for a work to be considered 'good' is anything but arbitrary. We call a theorists work 'good' if it makes predictions that agree with experiment, and those experiments are judged on whether they produce results that are reproducible by other independent experiments. It doesn't matter how you approach science, whether you use scribbles on paper or huge labs full of expensive microscopes, if it doesn't pass these criteria it's not only bad, it's useless.

I have deliberately left out any descriptions of the people behind the piano or doing the science. I did this because they are utterly irrelevant to the criteria of what constitutes good or bad work in a discipline. It does not matter if a black woman from, say, South London makes public a theory for some phenomenon by making use of novel computer simulation techniques, or whether a white man from, say, Princeton makes public an alternative theory using only one side of A4 with a few equations on it. Both works, to be classed as useful and 'good' science, will be judged by the same criteria.

Who does it ultimately doesn't matter. However, the fact that two different scientists from differing backgrounds, working on the same problem can only benefit progress on its solution. To make a crude analogy: an egg hunt with a handful of people who only know how to look in certain places with the same tools won't be that profitable, but add more people who look in different places with different tools and your egg hunt will be much more successful. 

Science is like this egg hunt. Increasing the diversity of scientists will only benefit science. However, in today's world science is not as diverse as one would like to think. Many institutions, departments, and labs are dominated by white men from similar backgrounds. Not that there is anything wrong with white men (from any background) but the lack of diversity is limiting the progress science could be making. Women and people of color are particularly absent in all echelons of science. There are certain institutional obstacles and barriers that discourage alternative students, post-docs, and early career researchers who want to do 'good' science from staying in science.

It is for the sake of 'good' science, finding those wondrous eggs brimming with natures secrets, that we must ensure those people from all walks of life, of all colors, and of all genders are met with open arms. This, however, is not the view held by everyone. There are those who claim that 'good' science can only be achieved by those who are superior in the various tasks that gets 'good' science done. They purport that only a certain kind of human is superior in doing science. Women and blacks, they say, are biologically disadvantaged in comparison to the white man in this respect and giving them equal opportunities will only slow down progress (basically they will be in the way).

There is not one credible shred of evidence that a person of a particular gender, color, and ethnicity is superior in any of the faculties that a 'good' scientist has. Even if it were true (it isn't) that white men are just that much sharper and better at certain tasks than everyone else, it still does not justify excluding or discriminating other people from doing science. Going back to our egg hunt analogy: if a group of white men with a certain background could compute various possible hiding spots and collect eggs much faster than everyone else, they would no doubt be beaten by a competing group containing those white men and people having different upbringing, genders, and ethnicity. This is because a group consisting of people from different backgrounds with various ways of thinking can conjecture about much more hiding spots and come up with more methods of how to get to them.

One could argue that since all types of human are innately capable of doing the tasks that lead to 'good' science, the only thing that makes people diverse are their various unique upbringings, experiences, and languages i.e. their background. In the egg hunt, if we were to have a group of white men each having a specific background that matches the diverse (different ethnicity and gender) group, then by my very own argument they should perform the same. This would be true of course, but as we know in real life it is highly unlikely that we would find a group of white men that have the same, upon accumulation, upbringing and experiences as a multi-ethnic and -gendered group.

Even if people of different ethnicity and gender all have the capability to perform scientific skills at the same level, they might still have slight phenotypical differences that would not be detected by some contrived test of these skills. Since work at the edge of science requires new thinking, normally in highly specialized and established fields, that breaks away from that of the past, any slight difference in thinking will confer an advantage. It therefore seems reasonable that a more diverse group of scientists is more likely to generate, at a faster pace, work that counts as 'good' science compared to that of a uniform group, with everything else being equal.

This argument is not restricted to humans, it just so happens that the species that can and want to do 'good' science are similar to us. If any other species or forms of life want to do 'good' science and are able to communicate with us, we will only be the better for it. Even a machine, the product of humans, may at some point in the future be able to do 'good' science in ways that we cannot as yet fathom. We should allow them to join in on our science too.

Anyone and anything that can play the piano, hunt for eggs, or do science should be encouraged by us to do so. Our music, bellies, and science will be forever richer for it.

A reply to Bloomfield: Towards a completely empirical foundation for veganism

Josef Bloomfield's essay [1] is a well written exposition of why one doesn't have a sound case to logically intertwine 'spiritualism', say asserting the existence of metaphysical souls of animals e.g., with veganism: the standpoint which has at its core the principle that manipulating animals for our sole benefit is inherently wrong. I want to almost push his arguments to their proper intended logical conclusion, which he doesn't quite get round to since the piece lacks the clear-cut empiricism and rationalism found only in the sciences.

One point that I would like to make is that whilst reading the piece which continually states how veganism cannot be conflated with spirituality, I was almost dumbfounded to find this in the conclusive paragraph:

To conclude, if spirituality and veganism exist in a symbiotic relationship, this can only be a good thing. If a spiritual or religious person feels motivated by their spiritual beliefs to become vegan, we should embrace them. - Josef Bloomfield

which, to me, contradicts the whole previous build up. Obviously this probably wasn't intentional, but it is slightly confusing since the penultimate paragraph reads:

This approach has to be secular. Secular abolitionist vegan moral philosophy does not require one to reject any other beliefs, other than that animals are ours to use. The audience will not react against secular justice in the way they would against spiritual. A spiritual argument can quickly descend into religious debate, which is an area of debate that would be best to avoid. - Josef Bloomfield

So which way is it?  I believe the apparent contradiction and confusion arises intrinsically from the way many vegans justify their adherence to the principle(s) of  veganism.

Jo asserts that it is so easy and so blindingly obvious that the use of animals for food and other products is 'morally wrong';

It doesn’t take much coherent thought to realise that the use of animals is morally wrong. - Josef Bloomfield

but this is a logical fallacy. He is justifying the statement: 'the use of animals is morally wrong' because.. well...  isn't it obvious!?  It is similar to justifying that the objects we see are a superposition of quantum states in the classical limit because... well..  isn't it so darn obvious!?

He doesn't provide a logical or scientific justification for the main premise of veganism. This is very dangerous, it means that any vegan who thinks the same way cannot adequately defend the core of their beliefs. It is also harder to convert non-vegans who may be logically inclined (quite a lot of people) because they may just think that veganism is based on a lifestyle choice which won't necessarily, at face value, improve their lives.

One could argue that, on some animal inclusive happiness principle, it is morally justified. Since reducing the animals un-happiness and pain equates to a greater score of total happiness for all animal kind. The happiness principle has its shortcomings...  what counts as happiness? Different animals, including us, experience mental states of pain and pleasure differently so how can we derive an averaged happiness measure?  Also all seemingly sophisticated moral philosophies around justifying veganism are actually just sugar coated expressions of empathy.

Humans (some more so than others) are programmed genetically to experience empathy when our young are in pain, so that we take better care of them so that our genes are more likely to live on. This empathy facility affects us when animals are in pain too, this is because there has been no selection pressure to distinguish specific human pain from animals...  any pain like behaviour is sufficient to induce empathy.  So, my argument continues, moral stances of veganism reduce to this empathy facility. Many vegans are vegan because they feel empathy when they are shown terrible (and believe me they are terrible) videos of slaughtering, chicks being blended etc.

However this is not a valid logical justification to accept a moral ideology. As heart warming as it is to stand alongside those who base their moral actions on empathy, it is primitive and contradictory to our modern secular system. It is primitive because in this time we understand that to live a in a free, healthy and progressive society we must advocate science, not because it feels right, but because it works. Our emotions are prone to error and we have much more refined and rigorous tools of reasoning at our feet to use.

Towards a valid foundation

I would openly claim that veganism is irrational because it is spiritual, and therefore I would never be vegan. - Josef Bloomfield

Replace 'spiritual' with 'emotional' and, from the preceding arguments, you can see how some people would still reject veganism because they may see that at the heart of all the moral 'stuff' is irrational emotion. Before anyone shouts 'how can emotion be irrational?' you must remember that anything rational can either be a system of logical axioms (maths) or based on experimental induction. Emotion by its very nature precedes sophisticated language and is built up from instincts ingrained within our brains from billions of years of natural selection.

So where are we now?  We need to place veganism on a foundation where, like Josef rightly says, it appeals to the rational faculty within us. Since veganism involves the real world, the only area that can help us is the realm of science. We must base veganism on facts.

What will change if we base veganism on facts and what type of facts anyhow?

 Well there is vast evidence pointing towards the hypothesis that eating meat will greatly increase your risks for chronic diseases which of course include the cardiovascular form [2]. It has been shown that dietary choices  account for 30% of factors leading to cancer in Western societies, a study concluded that vegan diets lowered the risk of getting cancer by a significant amount [2 - cancer]. Veganism is a form of food restriction, you are avoiding meat cuisines, which isn't all so bad since any form of food restriction (not leading to nutritional deficiency) and increase in antioxidants from increased veg intake actually increases health [2 - vegetarian].


Grazing animals consumes huge amounts of food and land. There are many future problems which could affect you, your children... but mainly YOU in the future. Global warming is a prevailing issue which is serious and the meat industry plays a bigger role than you would have thought in ruining this planet. There will come a time when we have to invest in technologies which remove carbon from the atmosphere, this will be when you are still alive. The countries you live in will have to pay for this, this means you will via tax. So by reducing your meat consumption you will inevitably save money in the future and preserve that fresh(ish) air you love to breathe in when you wake up. By freeing up land used by animals after there population dwindles due to humans not forcing increased rates of birth, this land can be used for green urban areas which will help the growing population find living space but still make the world greener. Plus less methane being produced!!!  For articles and papers for veganism and the environment see [3].

It is facts like these and growing evidence that a plant based diet will help you live a healthier, happier life, internally and externally in terms of the environment you live in. So since denying scientific fact is a sign of insanity, which not many people are(?), and actually realising that by accepting these facts and adapting to them, via veganism or even just reduced meat consumption for starters, you will help yourself. This is pretty much the empirical foundation for modern veganism, or what it should be.

It works because the facts align with our genetic disposition to survive, to procreate and live healthy lives but also due to the pressures of becoming successful in modern day living. To become successful in any field of note requires alertness, clear thinking and energy...  all this emulates from a properly functioning brain and body. Plus having a scientific mindset, which respects facts when they are properly established, will enable you to adapt quickly to the ever complex realm of technology, medicine and society.

So now we see that veganism is not based on spirituality or emotional empathy (or moral philosophy you say?) but it is based on impartial fact. Facts do not require belief, they will remain a fact even if people do not take to it.. but those who deny will be at a disadvantage for it. People who accept facts and adapt to them will most likely thrive and become successful... with the propensity to do so happens to be installed in our genes and within Western culture.

So will you dine with the carnivores or take your first steps to a healthier, greener and scientifically literate you?



[1] http://www.ecorazzi.com/2016/09/20/spirituality-and-veganism-may-co-exist-but-cannot-be-conflated/
[2] Science for plant based diets:

http://care.diabetesjournals.org/content/29/8/1777.short - diabetes
http://www.ncbi.nlm.nih.gov/pubmed/23169929 - cancer
http://europepmc.org/abstract/med/19166134 - vegetarianism- food restriction

[3]Science for plant based diets and the environment:

http://ajcn.nutrition.org/content/89/5/1699S.short

http://www.peta.org/issues/animals-used-for-food/global-warming/ - PETA

Could your genes make you racist ?

A  frightening awakening

The shocking result of the EU referendum has left remainers weeping in their pillows, the pound falling down the stairs and the xenophobic standing tall and proud. Politics has been truly shaken at its heart with the prime minister resigning and economic emotions flying high with no where to land.

One side effect of the success of the leave campaign has seen an emphatic spread of 'hate crime' and xenophobic outbreaks towards the Muslim, Polish and foreign community. I can only assume those who hold such dire and inhuman views believe that because a slight majority voted for leave it somehow justifies their actions towards benevolent, tax paying and culturally diverse citizens.

Racist graffiti was observed on the front entrance of the Polish Social and Cultural Association (POSK) in Hammersmith which is a direct act of hate crime.

This recent spout of such acts has been encouraged by Brexit but the hate and despise of immigrants and people of differing culture and ethnicity has been bubbling in many Brits minds for years. This is merely an opportune moment to strike. The leave campaign, whilst not explicitly promoting racism, has re-triggered the emotions and motives of many racist groups and in this sense it has been an absolute devastation in terms of dividing Britain.

Polish people have been migrating to the UK since world war II and Polish is the third most common language spoken here in Britain. I went to school with many Polish children and they have integrated within many communities very well, their stores and food becoming ever more popular with typical 'British' people.

The classic thing to say is that many working class people believe their future labour is being snatched away by immigrants and the like, they assert that immigrants should be put second place to them on the job market even if they are more hard working and cheaper labour. However many racist people do not just hate one single community of people, say just Polish or Muslim, but any community which differs to theirs. It seems to extend beyond jobs, fear of terrorism or religion but towards an innate hatred to that which is different to them.

Is there something...  biological going on here?

The Gene hath you by thy neck

Genes provide the instructions for proteins which dictate how your body develops and how it functions. They are the main stars in the show known as evolution and we are merely the vehicles, carrying them on generation after generation.

Now anything your genes instruct (to produce your phenotype) has been selected over great expanses of time, so the behaviours and biological make up of humans must serve a purpose to help propel genes into further generations. We can ask whether there would be any obvious advantages to having a gene, or collection thereof, which encourages a human to stick with other humans who look like it and who come from the same territory. 

If someone has the same skin tone as you and was born in the same place as you it is more than likely that they share more genes with you than say, a dark outsider. This means if you were to protect those who are physically more like you etc. from competing outsiders then similar genes will be more likely to be passed on to the next generation. This makes quite a lot of sense in terms of selfish genes. 

Potentially the selection mechanism for this wouldn't have to be extremely strong, maybe it was enough only to have genes which share resources with similar humans and protect them from danger in particular... it doesn't necessarily have to encourage the hunting of different humans.

Maybe the wide spreading of xenophobia and racism around the world is based upon a common inherited 'racist' gene. Obviously not everyone has this potential gene expressed in them as we see tolerant and multicultural societies existing in our modern world... but maybe because this gene was suppressed by other genetic factors? The environment? Or modern ideologies overriding genetic dispositions?

We can surely question the selective advantage of such a gene, if it were to exist. I proposed early that it may be advantageous for humans to protect those who are physically similar to them, in case they share the same genes. This would, in theory, increase the copies of that gene in the next generation. 

If we consider a small community who only breeds with themselves, under the influence of this said gene, then they will eventually become inbred and increase homozygotsity within cells (duplicate alleles of the gene present). There have been numerous reports of birth defects, learning difficulties and weakened defences of the inbred. 

These defects would surely put the human at a disadvantage in terms of producing offspring, whether it struggles to survive in order to mate or simply it is not sexually attractive, hence those genes will become less frequent within the gene pool.

There is growing evidence that intermixing i.e. interracial breeding which produces heterozygotsity within the cell increases parasite, disease and other harmful disorder resistance  (Professor Bill Amos - Cambridge) also a trait which produces more symmetrical facial structures occurs more in mixed raced adults (Dr Mark Shriver - Penn State).  In fact, many of us find humans of the opposite or same sex attractive solely because they are different... there seems to be a genetic advantage in this view too.

So there could potentially be a gene which protects those similar to oneself however the selective advantages are not convincing and it cannot explain how waves of racist people arise in modern societies, it surely must be something cultural not entirely, if at all, based on genes. Genes can encourage aggression, intelligence and many other things but something like xenophobia and nationalism is surely a cultural phenomenon and we must therefore bring in the right technical Cavalry. 

What do you meme it's me? 

Drawing analogies with the gene, the meme is the cultural unit in which a new form of evolution acts upon. Memes can be considered to be ideas, literal internet memes, snippets of music, art, isms and fashion accessories. Anything that can be imitated and copied by other humans acts as a meme. 

To illustrate the concept quickly just imagine 4 people on the tube, one starts humming a coldplay song, the other hums too but messes up a few times and the others copy him and so forth. The small errors in imitation lead to mutations of that meme. This means memes get passed on (like genes), have variation (like genes) and instruct (like genes) .... all this necessitates a selection process.

Now back to racism. Think of our modern and complex culture as a huge ensemble of memes living in subsystems called meme-pools which consist of memes competing with each other to be copied from human brain to brain. Now maybe it is possible that ideas based on xenophobia, while seemingly created by radical politicians from history etc. , have in fact evolved (in a meme-like fashion) so as to manipulate human brains to copy it.

The idea instructing its brain to be hostile of foreign ideas and values in such a way as to protect itself and fellow cooperating memes such as fundamentalist religion, right wing politics, fascism and nationalism. The idea manipulates the human into sharing it for its own survival without seemingly benefiting those who believe it.

This would mean racism is not innate but acquired through different forms of imitation and it is spread culturally. Memes arising from tolerance, reason and inclusion directly pose a competitive threat these xenophobic memes and hence a clash occurs (we are obviously in the midst of such a clash now). 

Thinking in terms of memes and culture this way is very different to how we normally think of things, it could offer a unique and potentially scientifically interesting perspective into how cultural trends and political movements work. Also it could offer an explanation to how many people acquire ideas and how ideas seem to take control of them, making them do acts which do not directly benefit them economically or in terms of passing their genes on.

It could be a mixture of genetic dispositions and memes taking advantage of these, two distinct replicators manipulating humans for their own endeavour. Only future advancements in understanding many-human-systems, genetics and even memetics will lead to more specific and clear answers to these interesting questions.

All I can say is this...   multiculturalism and the diversification of ethnicity and language brings great benefits to societies in terms of  advancement in knowledge, peace and genetic prosperity. 

LOVE ALL DESPITE THEIR DIFFERENCES!

  

The Protein Folding Problem

What is a protein?

  Most people are familiar with the word protein because quite a lot of food has it and protein, as we are told, is good for muscular recovery. But proteins are much more than that. Without them our body couldn't function at all, they are the diverse workers which reside in our cells and allow our food to be digested properly, our brain to function to its full potential and to avoid our muscles wasting away.

Proteins are polymers, meaning they are strings of repeating subunits called monomers. Monomers are the basic units of proteins and consist of a class of 21 amino acids:

These different amino acids bond together via N = H or C = O hydrogen bonding to form the lengthy protein chains. This bonding is due to a chemical reaction. As you can see, there are many amino acids so the natural question to ask is: does the ordering of amino acids matter ?  The answer to that question is a huge yes! It matters because different amino acid sequences lead to different folded states of the protein polymer chain. These different folded states result in the protein doing a different job. If proteins folded the same way irrespective of their amino acid sequencing life as we know it could not have evolved all those billions of years ago. 

It is compelling to note that DNA, the helix molecule which contains the important genetic code, has a structure which does NOT depend on the sequence of the bases inside the helix. This fact ensures the helix molecule can be used as an efficient information storage medium. 

So what's the problem?

So we  have gathered that proteins are important and their folded structure depends on the sequence of the amino acids along the chain. The problem here is what causes the protein, which is initially a floating spaghetti like structure in water, to fold? Most useful proteins in biological organisms contain very long chains of amino acids and have a huge amount of possible states that they could be in. Theoretically it would take the protein to make trial and error movements, testing each possible state, before finding the right 'native' state which it needs to be in to do its job.

This would require huge expanses of time, obviously evolution would have sieved this out in the very early stages of life.... and in a sense it did. It is experimentally known that proteins fold on a time scale of milliseconds to seconds, which presents a paradox...  how does the protein get into the 'native state' without testing all or most of the possible states. This is known as Levinthal's paradox.

It is assumed (yes only assumed) in the general statistical physics and chemical community that what helps proteins fold so quickly is thermodynamics. In particular the driving force for protein folding is entropy, a measure of disorder, and hence a minimization of a quantity known as the Gibbs free energy. The protein chain starts out as an ordered linear string and due to most of the bases being hydrophobic (repelling water) the water around it forms ice like cages which forces the protein into a more compact shape. This most compact and stable of these shapes is called the 'native state' and it is the state which has the lowest Gibbs free energy. 

However all is not simple. There is not just one simple minimum for proteins. The minima of the Gibbs free energy function form a rough landscape full of different wells of differing depth. As the protein is also undergoing brownian fluctuations but also being forced into compact globules by the hydrophobic bases it travels through this energy landscape. Sometimes its 'shape' gets stuck due to it being in a temporary minimmum well but this may not be the most stable and the shape is relaxed slightly until being forced into another compact shape determined by yet another minimum well.

In reality the forces causing the protein to fold have to interact on a atomistic level, the atoms of the water solution interact with the atoms of the bases of the protein. To simulate these atomistic collisions is an extremely computational problem, which requires taking into account the position of many many particles and computing huge amounts of tiny interactions. These simulations are called molecular dynamics and some ingenious approximations have been made but to simulate a whole protein fold solely based on molecular dynamics is.. quite simply... near impossible currently.

So there are many problems...

1. How can we prove analytically that proteins really do fold because they want to minimize their Gibbs free energy?
2. How much computer power does it take to fully simulate, at an atomic level, the protein during folding?
3. Can we fully replicate the stability of the folded protein in real time?
4. Can we form any program which... given the sequence of amino acids could determine an immediate folded state?

These are some of the pressing questions in the field of theoretical and computational protein folding. Is there another computationally inexpensive way to do this?

Taking a step back, then compute the acceptance probability

One way which is reviving the field is to not focus on the computationally heavy molecular dynamics.. but to attack the density of states directly. Since it is okay to assume the native state is at a minimum of some Gibbsian like energy function, we can simply sample the density of states and 'roam' the free energy landscape until we hit the deepest minimum.

This can be done using specialized Monte Carlo techniques e.g. umbrella sampling and Wang Landau algorithms. These techniques start from a partition function (which counts all possible states of a system) and begins to sample the density of states by making trial changes to the system i.e. moving a part of the protein to another point and seeing if it is energetically favorable according to some acceptance criterion. If you are interested in Monte Carlo algorithms I recommend reading the original paper by Metropolis, Rosentbluth and Teller on the Metropolis algorithm.

In the field today there are improvements to Monte Carlo algorithms which allow bigger systems to be simulated and a better sampling of the free energy landscape. 

All in all it is a very exciting area of research one which has huge biological significance and could impact our medical world.