Archive for the ‘genetics’ Category
epigenetics and imprinting 7: more problems, and ICRs
the only image I can find that I really understand
In the previous post in this series I wrote about the connection between two serious disorders, Angelman syndrome and Prader-Willi syndrome, their connection to a missing small section of chromosome 15, and how they’re related to parental inheritance. These syndromes can sometimes also be traced back to uniparental disomy, in which the section of chromosome 15 is intact, but both copies are inherited from the mother (resulting in PWS) or the father (resulting in AS).
So the key here is that this small section of chromosome 15 needs to be inherited in the correct way because of the imprinting that comes with it. To take it to the genetic level, UBE3A is a gene which is only expressed from the maternal copy of chromosome 15. If that gene is missing in the maternal copy, or if, due to uniparental disomy, both copies of the chromosome are inherited from the father, UBE3A protein won’t be produced and symptoms of Angelman syndrome will appear. Similarly, PWS will develop if a certain imprinted gene or genes aren’t inherited from the father. Other imprinting disorders have been found, for example, one that leads to Beckwith-Wiedemann syndrome, though the mechanism of action is different, in that both copies of a gene on chromosome 11 are switched on when only the paternal copy should be expressed. This results in abnormal growth (too much growth) in the foetus. It too has an ‘opposite’ syndrome, Silver-Russell syndrome, in which the relevant protein expression is reduced, resulting in retarded growth and dwarfism.
But now to the question of exactly how genes are switched on and off, or expressed and repressed. DNA methylation, briefly explained in my first post on this topic, is essential to this. Methyl groups are carbon-hydrogen compounds which can be bound to a gene to switch it off, but here’s where I start to get confused. I’ll quote Carey and try to make sense of it:
… it may be surprising to learn that it is often not the gene body that is methylated. The part of the gene that codes for protein is epigenetically broadly the same when we compare the maternal and paternal copies of the chromosome. It’s the region of the chromosome that controls the expression of the gene that is differently methylated between the two genomes.
N Carey, The epigenetics revolution, 2011 p140
The idea, I now realise, is that there’s a section of the chromosome that controls the part of the gene that codes for the protein and it’s this region that’s differently methylated. Such regions are called imprinting control regions (ICRs). Sometimes this is straightforward, but it can get extremely complicated, with whole clusters of imprinted genes on a stretch of chromosome, being expressed from the maternally or paternally derived chromosomes, and not simply through methylation. An ICR may operate over a large region, creating ‘roadblocks’, keeping different sets of genes apart, and affecting thousands of base-pairs, not always in the same way. Repressed genes may come together in a ‘chromatin knot’, while other, activated genes from the same region form separate bundles.
Imprinting is a feature of brain cells – something which, as of the writing of Carey’s book (2011), is a bit of a mystery. Not so surprising is the number of expressed imprinted genes in the placenta, a place where competing paternal-maternal demands are played out. As to what is going on in the brain, Carey writes this:
Professor Gudrun Moore of University College London has made an intriguing suggestion. She has proposed that the high levels of imprinting in the brain represents a post-natal continuation of the war of the sexes. She has speculated that some brain imprints are an attempt by the paternal genome to promote behaviour in young offspring that will stimulate the mother to continue to drain her own resources, for example by prolonged breastfeeding.
N Carey, The epigenetics revolution, 2011. pp141-2
This sounds pretty amazing, but it’s a new epigenetic world we’re exploring. I’ll explore more of it next time.
References
The epigenetics revolution, by Nessa Carey, 2011
a DNA dialogue 3: two anti-parallel strands
Jacinta: Ok so these two strands of DNA are described as anti-parallel. Is this just intended to confuse us?
Canto: Apparently not, in fact it’s quite essential. The useful q&a site Quora has good info on this, and understanding it in all its complexity should help us to understand DNA general – it’s one of a thousand useful entry points.
Jacinta: Yes, and I’ll try to explain. It became clear to us last time that the strands or ribbons twisted round in a double helix, called the backbone of the molecule, are made from phosphate and deoxyribose sugar, covalently bonded together. That means tightly bonded. Between the two strands, connecting them like ladder rungs, are nitrogenous bases (this is new to us). That’s adenine, thymine, guanine and cytosine, bonded together – A always to T, and C to G – with weak hydrogen bonds. We’ll have to look at why they must be paired in this way later.
Canto: It’s called Chargaff’s base pairing rule, which doesn’t tell us much.
Jacinta: And, according to a respondent from Quora, ‘the two strands of DNA are anti-parallel to each other. One of them is called leading strand, the other is lagging strand’. But I don’t quite get this. How are there two strands of DNA? I thought there was one strand with two sugar-phosphate backbones, and a rung made up of two – nitrogenous nucleobases? – weakly connected by hydrogen bonds.
Canto: I think the idea is there are two strands, with the attached bases, one next to another on the strand, and weakly attached to another base, or set of bases each attached to another phosphate-sugar backbone. As to why the whole thing twists, rather than just being a straight up-and-down ladder thing, I’ve no idea. Clearly we’re a couple of dopey beginners.
Jacinta: Well, many of the Quora respondents have been teaching molecular biology for years or are working in the field, and just skimming through, there’s a lot be learned. For now, being anti-parallel is essential for DNA replication – which makes it essential to DNA’s whole purpose if I can call it that. I’ll also just say that the sugars in the backbone have directionality, so that the way everything is structured, one strand has to go in the opposite direction for the replication to work. If for example the strands were facing in the same direction, then the base on one side would connect to a hydrophobic sugar (a good thing) but the base on the other side would be facing a hydrophilic phosphate (a bad thing). Each base needs to bond with a sugar – that’s to say a carbon atom, sugar being carbon-based – so one strand needs to be an inversion of the other. That’s part of the explanation.
Canto: Yes, I find many of the explanations are more like descriptions – they assume a lot of knowledge. For example one respondent says that the base pairs follow Chargaff’s rule and that means purines always pair up with pyrmidines. Not very helpful, unless maybe you’re rote-learning for a test. It certainly doesn’t explain anti-parallelism.
Jacinta: Well, although we don’t fully understand it yet, it’s a bit clearer. Anti-parallelism is an awkward term because it might imply, to the unwary, something very different from being parallel. The strands are actually parallel but facing in the opposite direction, and when you think about the structure, the reason for that becomes clearer. And imagining those backbone strands facing in the same direction immediately shows you the problem, I think.
Canto: Yes and for more insight into all that, we’ll need to look more closely at pyrmidines and purines and the molecular structure of the backbone, and those bases, and maybe this fellow Chargaff.
References
epigenetics and imprinting 5: mouse experiments and chromosome 11
So we were looking at how we – mammals amongst others – are engaged in a kind of battle for the best way to ensure our genetic survival into the future, beyond our insignificant little selves. This battle begins in the very early phase of life, as zygotes multiply to form a blastocyst.
Remember from my last post on this topic, the male mammal is interested in the offspring above all else. He’s even happy to sacrifice the mother for the sake of the child – after all there’s plenty more fish in the sea (or mammals in the – you know what I mean). The female, on the other hand, is more interested in self-preservation than in this pregnancy. She wants more than one chance to pass on her genes.
So, by the blastocyst stage, cells have differentiated into those that will form the placenta and those that will form the embryo itself. Experiments on mice have helped to elucidate this male-female genetic struggle. Mouse zygotes were created which contained only paternal DNA and only maternal DNA. These different zygotes were implanted into the uterus of mice. As expected, the zygotes didn’t develop into living mice – it takes DNA from both sexes for that. The zygotes did develop though, but with serious abnormalities, which differed depending on whether they were ‘male’ or ‘female’. In those in which the chromosomes came from the mother, the placental tissues were particularly underdeveloped. For those with the male chromosomes, the embryo was in a bad way, but the placental tissues not so much.
In short, these and other experiments suggested that the male chromosomes favoured placental development while the female chromosomes favoured the embryo. Thus, the male chromosomes are ‘aiming’ to build up the placenta to drain as many nutrients as possible from the mother and feed them into the foetus. The female chromosomes have the opposite aim, resulting in a ‘fine balance’ in the best scenarios.
Further work in this area has identified particular chromosomes responsible for these developments, and some of the epigenetic factors involved. For example, mouse chromosome 11 is important for offspring development. When the offspring inherits a copy of chromosome 11 from each parent, the offspring will be of normal size. If both copies come from the mother it will abnormally small, while if both come from the father it will be abnormally large. These experiments were carried out on inbred mice with identical DNA. Nessa Carey summarises:
If you sequenced both copies of chromosome 11 in any of the three types of offspring, they would be exactly the same. They would contain the same millions of A, C, G and T base-pairs, in the same order. But the two copies of chromosome 11 do clearly behave differently at a functional level, as shown by the different sizes of the different types of mice. Therefore there must be epigenetic differences between the maternal and paternal copies of chromosome 11.
So this means that chromosome 11 is an imprinted chromosome – or at least certain sections of it. This is the same for other chromosomes, some of which aren’t imprinted at all. But how is it done? That’s the complex biochemical stuff, which I’ll try to elucidate in the next post on this topic.
Footnote: the photo above shows a bi-maternal mouse with healthy offspring, and further work in deleting imprinted genetic regions has allowed researchers to create healthy bi-paternal mice too. There’s a fascinating account of it here.
References:
Nessa Carey, The epigenetics revolution, 2011
https://www.the-scientist.com/news-opinion/first-mouse-embryos-made-from-two-fathers-64921
A DNA dialogue 1: the human genome
Canto: I’m often confused when I try to get my head around all the stuff about genes and DNA, and genomes and alleles and chromosomes, and XX and XY, and mitosis and meiosis, and dominant and recessive and so on. I’d like to get clear, if only I could.
Jacinta: That’s a big ask, and of course we’re both in the same boat. So let’s use the magical powers of the internet to find answers. For example, here’s something that confuses me. The Human Genome project, which ended around the year 2000, involved a mapping of the whole human genome, and that includes coding and non-coding genes, and I think it was found to contain 26,000 or so – what? Letters? Genes? Coding genes? Anyway there’s a number of questions there, but they’re not the questions that confuse me. I don’t get that we now, apparently, have worked out the genetic code for all humans, but each of us has different DNA. How, exactly, does our own individual DNA relate to the genome that determines the whole species? Presumably it’s some kind of subset?
Canto: Hmmm. This article from the Smithsonian tells us that the genetic difference between human individuals is very tiny, at around 0.1%. We humans differ from bonobos and chimps, two lineages of apes that separated much more recently, by about 1.2%….
Jacinta: Yes, yes, but how, with this tiny difference between us, are we able to use DNA forensically to identify individuals from a DNA sample?
Canto: Well, perhaps this Smithsonian article provides a clue. It says that the 1.2% difference between us and chimps reflects a particular way of counting. I won’t go into the details here but apparently another way of counting shows a 4-5% difference.
Jacinta: We probably do need to go into the details in the end, but clearly this tiny .1% difference between humans is enough for us to determine the DNA as coming from one individual rather than 7 to 8 billion others. Strangely enough, I can well believe that, given that we can detect gravitational waves and such – obviously using very different technology.
Canto: Yeah the magic of science. So the Human Genome Project was officially completed in April 2003. And here’s an interesting quote from Wikipedia:
The “genome” of any given individual is unique; mapping the “human genome” involved sequencing a small number of individuals and then assembling these together to get a complete sequence for each chromosome. Therefore, the finished human genome is a mosaic, not representing any one individual.
Of course it would have to be a mosaic, but how can it represent the whole human genome when it’s only drawn from a small number? And who were these individuals, how many, and where from?
Jacinta: The Wikipedia article does give more info on this. It tells us that the project isn’t really finished, as we’ve developed techniques and processes for faster and deeper analyses. As to your questions, when the ‘finished’ sequencing was announced, the mosaic was drawn from a small number of anonymous donors, all of European origin.
Canto: But we all originated from Africa anyway, so…
Jacinta: So maybe recent ‘origin’ isn’t so important. Anyway, that first sequencing is now known as the ‘reference genome’, but after that they did sequence the genomes of ‘multiple distinct ethnic groups’, so they’ve been busy. But here are some key findings, to finish off this first post. They found some 22,300 protein-coding genes, as well as a lot of what they used to call junk DNA – now known as non-coding DNA. That number is within the mammalian range for DNA, which no doubt surprised many. Another blow for human specialness? And they also found that there were many more segmental duplications than expected. That’s to say, sections of DNA that are almost identically repeated.We’ll have to explore the significance of this as we go along.
Canto: Yes, that’s enough for starters. Apparently our genome has over 3 billion nucleobase pairs, about which more later no doubt.
References
epigenetics and imprinting 4: the male-female thing
Gametes are gametes because of epigenetic modifications in their pro-nuclei, but they have to lose these modifications, or transform them, when they come together to form zygotes. The male pro-nucleus DNA methylation is stripped away immediately after sperm penetrates egg. The egg pronucleus undergoes the same process, but more gradually. It’s like a wiping away of epigenetic memory, creating totipotency, which becomes a more limited pluripotency as the blastocyst, with its inner cell mass (ICM), forms.
The ICM cells begin differentiating through the regulation of some key genes. For example, a gene codes for a protein that switches on a set of genes, which code for proteins in a cascading effect. But it’s not quite a matter of switching genes on or off, it’s rather more complex. The process is called gene reprogramming, and it’s of course done effortlessly during every reproductive cycle. Artificial reprogramming of the kind carried out by Yamanaka and others, an essential part of cloning, hasn’t come close to this natural process that goes on in mammals and other species every day.
Clearly, though the epigenetic reprogramming for the female pronucleus is different from that carried out more swiftly in the male. As Carey puts it, ‘the pattern of epigenetic modifications in sperm is one that allows the male pronucleus to be reprogrammed relatively easily.’ Human researchers haven’t been particularly successful in reprogramming an adult nucleus by various methods, such as transferring it to a fertilised egg or treating it with the four genes isolated by Yamanaka. The natural process of gene reprogramming eliminates most of the epigenetic effects accumulated in the parent genes, but as the reprogramming is a different process in the male and female pro-nucleus, this shows that they aren’t functionally equivalent. There is a ‘parent-of-origin effect’. Experiments done on mice to explore this effect found that DNA methylation, an important form of chromatin modification (and the first one discovered), was passed on to offspring by the female parent. That’s to say, DNA from the female was more heavily methylated than that from the male. Carey describes the DNA as ‘bar-coded’ as coming from the male or the female. The common term for this is imprinting, and it’s entirely epigenetic.
Imprinting has been cast by Carey, and no doubt others, as an aspect of the ‘battle of the sexes’. This battle may well be imprinted in the pronuclei of the fertilised egg. Here’s how Carey puts the two opposing positions:
Male: This pregnant female is carrying my genes in the form of this foetus. I may never mate with her again. I want my foetus to get as big as possible so that it has the greatest chance of passing on my genes.
Female: I want this foetus to pass on my genes. But I don’t want it to be at the cost of draining me so much that I never reproduce again. I want more than this one chance to pass on my genes.
So there’s a kind of balance that has developed in we eutherian mammals, in a battle to ensure that neither sex gains the upper hand. Further experiments on mice in recent times have explored how this battle is played out epigenetically. I’ll look at them in the next post in this series.
Reference
The Epigenetics Revolution, by Nessa Carey, 2011
epigenetics and imprinting 2: identical genes and non-identical phenotypes
I’ve now listened to a talk given by Nessa Carey (author of The epigenetic revolution) at the Royal Institution, but I don’t think she even mentioned imprinting, so I may not mention it again in this post, but I’ll get back to it.
The talk was of course easier to follow than the book, and it didn’t really teach me anything new, but it did hammer home some points that I should’ve mentioned at the outset, and that is that it’s obvious that genetics isn’t the whole story of our inheritance and development because it doesn’t begin to explain how, from one fertilised egg – the union of, or pairing of, two sets of chromosomes – we get, via divisions upon divisions upon divisions, a complex being with brain cells, blood cells, skin cells, liver cells and so forth, all with identical DNA. It also doesn’t explain how a maggot becomes a fly with the same set of genes (or a caterpillar becomes a butterfly, to be a little more uplifting). These transformations, which maintain genetic inheritance while involving massive change, must be instigated and shaped by something over and above genetics but intimately related to it – hence epigenetics. Other examples include whether a crocodile hatchling will turn out male or female – determined epigenetically via the temperature during development, rather than genetically via the Y chromosome in mammals.
So, to add to the description I gave last time, the histone proteins that the DNA wraps itself round come in batches or clusters of eight. The DNA wraps around one cluster, then another, and so on with millions of these histone clusters (which have much-studied ‘tails’ sticking out of them). And I should also remind myself that our DNA comes in a four-letter code strung together, out of which is constructed 3 billion or so letters.
The detailed description here is important (I hope). One gene will be wrapped around multiple histone clusters. Carey, in her talk, gave the example of a gene that breaks down alcohol faster in response to consumption over time. As Carey says, ‘[the body] has switched on higher expression of the gene that breaks down alcohol’. The response to this higher alcohol consumption is that signals are generated in the liver which induce modifications in the histone tails, which drive up gene expression. If you then reduce your alcohol consumption over time, further modifications will inhibit gene expression. And it won’t necessarily be a matter of off or on, but more like less or more, and the modifications may relate to perhaps an endless variety of other stimuli, so that it can get very complicated. We’re talking about modifications to proteins but there can also be modifications to DNA itself. These modifications are more permanent, generally. This is what creates specialised cells – it’s what prevents brain cells from creating haemoglobin, etc. Those genes are ‘tightened up’ or compacted in neurons by the modifying agents, so that, for example, they’re permanently unable to express the haemoglobin-creating function.
All of this is extremely fascinating and complex, of course, but the most fascinating – the most controversial and headline-creating stuff – has to do with carrying epigenetic changes to the next generation. The inheritance of acquired characteristics, no less. Next time.
References
What is epigenetics? with Nessa Carey – The Royal Institution (video)
The Epigenetics Revolution, by Nessa Carey, 2011
epigenetics and imprinting 1 – it’s complex
The last book I read was The Epigenetics Revolution by Nessa Carey, though I’m not sure if I’ve really read it. So much of it was about persisting with the next sentence though I hadn’t fully understood the previous one. Biochemistry does that to me – too many proteins, versions of RNA, transposons, transferases, suppressors, catalysers, adjuvants and acronyms. And in the end I’m not at all sure how much progress we’re making in this apparently tantalising field.
So I’m going to pick out imprinting for starters, as a way of familiarising myself a little more with the epigenetic process of leaving tabs or marks on specific genes.
I know nothing about imprinting. Isn’t it what female birds do with their offspring, even when they’re still in the shell? Here’s how Wikipedia introduces it :
Genomic imprinting is an epigenetic phenomenon that causes genes to be expressed in a parent-of-origin-specific manner. Forms of genomic imprinting have been demonstrated in fungi, plants and animals. As of 2014, there are about 150 imprinted genes known in the mouse and about half that in humans. Genomic imprinting is an inheritance process independent of the classical Mendelian inheritance. It is an epigenetic process that involves DNA methylation and histone methylation without altering the genetic sequence. These epigenetic marks are established (“imprinted”) in the germline (sperm or egg cells) of the parents and are maintained through mitotic cell divisions in the somatic cells of an organism.
This suggests that it’s not something life-forms do, it just happens. But there are a number of mysterious terms here that need exploring – ‘a parent-of-origin-specific manner’, ‘DNA methylation’ and ‘histone methylation’.
Briefly, to get all that DNA (between 2 and 3 metres to each nucleus) to fit inside that tiny space you need some expert packaging, and that’s where histones come in. They’re proteins that DNA gets wound around, like cotton reels, and together the histones and the DNA are called chromatin. They’re also divided into sections called nucleosomes.
DNA methylation is when a methyl group, derived from methane (CH3), is added to the DNA, affecting its activity, including repressing gene transcription. Histone methylation is when methyl groups are added to amino acids in histone proteins. Again these can repress or enhance gene transcription, depending on the amino acids and how they’re methylated.
The parent-of-origin thing is most interesting to me, and needs a bit more explaining. When a human sperm cell enters an egg cell, as the first step in fertilisation, it carries its load of 23 chromosomes in what is called a pro-nucleus. In a sense a sperm cell, much smaller than an egg, is nothing but a pro-nucleus surrounded by a membrane, with a tail for motility. Once inside the egg, the tail and the membrane are shed. The egg cell also has its load of 23 chromosomes in its pro-nucleus, but this is considerably larger than the male – and the human egg cell in its entirety has about 100,000 times the volume of a sperm cell. The point is that the differences in the male and female pro-nuclei have a lot to do with epigenetic effects including imprinting, which affect phenotypic traits, including disease prone-ness and structural effects in animals and plants. Tracing these effects in molecular terms to either parent therefore becomes a priority.
So, this is a little starter in what is an overwhelmingly complex topic. I shall return to it.
On Massimo Pigliucci on scientism: part 1 – what is science?
I’ve written a couple of posts on scientism (all references below), which is for some reason a topic that always gets me exercised. So a recent brief interview with the philosopher Massimo Pigliucci, on the Point of Inquiry podcast, has set me back on the wagon. This blog post will be a piece by piece analysis of (some bits of) the interview.
I’ll begin with the Point of Inquiry host Kavin Senapathy’s intro, in which she gives a definition of scientism as:
this idea that the scientific method is the only worthwhile way of answering questions, and that any question that can’t be tackled using science is therefore unimportant or frivolous, and this often seems to apply to areas of social or political concern. In practice, those with a scientific approach try to colonise other areas of expertise and call them science. So this is really an ideology
So scientism is an ideology (and Pigliucci agrees with this later in the interview). I must say I’m skeptical of both terms, but let me focus for now on ‘ideology’. I once recall, during a meeting of secular and religious humanists, an old bloke beside me describing atheism as an ideology. The term’s often abused, and almost invariably used as a put-down. Only the other day, our former PM, John Howard, not known for his scientific literacy, complained that the recent federal election was marred by ‘climate change ideology’, by which he clearly meant the view that anthropogenic global warming is an issue.
More important here, though, is the attempt to define scientism, which makes me wonder if scientism is really a thing at all. The problem for me here is that it’s obvious that any area of ‘social or political concern’ will benefit from rigorous thought, or inference, based on various forms of evidence. Whether you want to call it science or not isn’t, for me, a major issue. For example, a state’s immigration policy would best be based on a range of concerns and analyses about its population, its resources, its productivity, its degree of integration, its previous experience of immigration, its relations with neighbours, the needs and aspirations of the immigrants, and so on. These factors can’t simply be intuited (though politicians generally do base their decisions on intuition, or ideology), but whether such analysis rises to the level of science doubtless depends on how you define science. However, it would clearly benefit from science in the form of number-crunching computer technology – always bearing in mind the garbage-in-garbage-out caveat.
So, it’s not about ‘colonising’ – it’s about applying more rigour, and more questioning, to every area of human activity. And this is why ‘scientism’ is often a term of abuse used by the religious, and by ‘alternative medicine’ and ‘new age’ aficionados, who are always more interested in converts than critiques.
Returning to the interview, Pigliucci was asked first off whether it’s a common misconception among skeptics that there’s a thing called ‘the scientific method’:
Yes I think it is, and it’s actually a common misconception among scientists, which is more worrisome. If you pick up a typical science textbook… it usually starts out with a short section on the scientific method, by which they usually mean some version of… the nomological deductive model. The idea is that science is based firstly on laws…. the discovery of laws of nature, and ‘deductive’ means that mostly what is done is deduction, the kind of inferential reasoning that mathematicians and logicians do. But no scientists have ever used this model, and philosophers of science have debated the issue over the last century of so and now the consensus among such philosophers is that scientists do whatever the hell works….
(I’ve ‘smoothed out’ the actual words of Pigliucci here and elsewhere, but I believe I’ve represented his ideas accurately). I found this an extraordinary confession, by a philosopher of science, that after a century of theorising, philosophers have failed abysmally in trying to define the parameters of the scientific process. I’m not sure if Pigliucci understands the significance, for his own profession, of what he’s claiming here.
I have no problems with Pigliucci’s description that scientists ‘do what works’, though I think there’s a little more to it than that. Interestingly, I read a few books and essays on the philosophy of science way back in my youth, before I actually started reading popular science books and magazines, and once I plugged into the world of actual scientific experimentation and discovery I was rarely tempted to read that kind of philosophy again (mainly because scientists and science writers tend to do their own practical philosophising about the field they focus on, which is usually more relevant than the work of academic philosophers). I came up, years ago, with my own amateur description of the scientific process, which I’ll raise here to the status of Universal Law:
Scientists employ an open-ended set of methods to arrive at reliable and confirmable knowledge about the world.
So, while there’s no single scientific method, methodology is vital to good science, for hopefully obvious reasons. Arriving at this definition doesn’t require much in the way of philosophical training, so I rather sympathise with those, such as Neil Degrasse Tyson, Sam Harris and Richard Dawkins, who are targeted by Pigliucci as promoters or practitioners of scientism (largely because they feel much in the philosophy of science is irrelevant to their field). But first we really need to get a clearer view of what Pigliucci means by the term. Here’s his attempt at a definition:
Scientism is the notion that some people apply science where either it doesn’t belong or it’s not particularly useful. So, as betrayed by the ‘ism’, it’s an ideology. It’s the notion that it’s an all-powerful activity and that all interesting questions should be reducible to scientific questions. If they’re not, if science can’t tell you anything, then either the question is uninteresting or incoherent. This description of scientism is generally seen as a critique, though there are some who see scientism as a badge of honour.
Now I must say that I first came across scientism in this critical sense, while watching a collection of speeches by Christians and pro-religion philosophers getting stuck into ye olde ‘new atheism’ (see the references below). Their views were of course very defensive, and not very sophisticated IMHO, but scientism was clearly being used to shelter religious beliefs, which cover everything from morality to cosmology, from any sort of critique. There was also a lot of bristling about scientific investigations of religion, which raises the question, I suppose, as to whether anthropology is a science. It’s obvious enough that some anthropological analyses are more rigorous than others, but again, I wouldn’t lose any sleep over such questions.
But the beauty of the scientific quest is that every ‘answer’ opens up new questions. Good science is always productive of further science. For example, when we reliably learned that genes and their ‘mutations’ were the source of the random variation essential to the Darwin-Wallace theory of evolution, myriad questions were raised about the molecular structure of genes, where they were to be found, how they were transferred from parents to offspring, how they brought about replication and variation, and so forth. Science is like that, the gift that keeps on giving, turning ‘unknown unknowns’ into ‘known unknowns’ on a regular basis.
I’ve read countless books of ‘popular’ science – actually many of them, such as Robert Sapolsky’s Behave, James Gleick’s The information, and Oliver Morton’s Eating the the sun, are fiendishly complex, so not particularly ‘popular’ – as well as a ton of New Scientist, Scientific American and Cosmos magazines, and no mention has been made of ‘the scientific method’ in any of them, so Pigliucci’s claim that many scientists believe in some specific method just doesn’t ring true to me. But let me turn to some more specific critiques.
When Sam Harris wrote The Moral Landscape…he wrote in an endnote to the book that by science he meant any kind of reasoning that is informed by facts. Well, by that standard when my grandmother used to make mushroom risotto for me on Sundays, she was using science, because she was reasoning about what to do, based on factual experience. Surely that doesn’t count as science [laughing]… Even if you think of ‘food science’ as a science that’s definitely not what my grandmother was doing. It’s this attempt to colonise other areas of expertise and call them science…
In my view Pigliucci disastrously misses the point here. Making a delicious risotto is all about method, as is conducting an effective scientific experiment. It’s not metaphorical to say that every act of cooking is a scientific experiment – though of course if you apply the same method to the same ingredients, MacDonalds-style, the experimental element diminishes pretty rapidly. Once someone, or some group, work out how to make a delicious mushroom risotto (I’m glad Pigliucci chose this example as I’ve cooked this dish countless times myself!) they can set down the recipe – usually in two parts, ingredients and method – so that it can be more or less replicated by anyone. Similarly, once scientists and technologists work out how to construct a functioning computer, they can set down a ‘computer recipe’ (components and method of construction) so that it can be mass-produced. There’s barely any daylight between the two processes. The first bread-makers arguably advanced human technology as much as did the first computer-makers.
I have quite a bit more to say, so I’ll break this essay into two parts. More soon.
References – apart from the first and the last, these are all to pieces written by me.
Point of Inquiry interview with Massimo Pigliucci
Discussion on scientific progress and scientism, posted April 2019
A post about truth, knowledge and other heavy stuff, posted March 2013
politics and science need to mix, posted August 2011
On supervenience, posted January 2011
Roger Scruton and the atheist ‘fashion’, posted January 2011
a critique of Johnathan Ree’s contribution, posted January 2011
Marilynne Robinson tries her hand at taking on ‘new atheism’, posted January 2011
kin selection – some fascinating stuff
Canto: So we’ve done four blogs on Palestine and we’ve barely scratched the surface, but we’re having trouble going forward with that project because, frankly, it’s so depressing and anger-inducing that it’s affecting our well-being.
Jacinta: Yes, an undoubtedly selfish excuse, but we do plan to go on with that project – we’re definitely not abandoning it, and meanwhile we should recommend such books as Tears for Tarshiha by the Palestinian peace activist Olfat Mahmoud, and Goliath by the Jewish American journalist Max Blumenthal, which highlight the sufferings of Palestinian people in diaspora, and the major stresses of trying to exist under zionist monoculturalism. But for now, something completely different, we’re going to delve into the fascinating facts around kin selection, with thanks to Robert Sapolski’s landmark book Behave.
Canto: The term ‘kin selection’ was first used by John Maynard Smith in the early sixties but it was first mooted by Darwin (who got it right about honey bees), and its mathematics were worked out back in the 1930s.
Jacinta: What’s immediately interesting to me is that we humans tend to think we alone know who our kin are, especially our extended or most distant kin, because only we know about aunties, uncles and second and third cousins. We have language and writing and record-keeping, so we can keep track of those things as no other creatures can. But it’s our genes that are the key to kin selection, not our brains.
Canto: Yes, and let’s start with distinguishing between kin selection and group selection, which Sapolsky deals with well. Group selection, popularised in the sixties by the evolutionary biologist V C Wynne-Edwards and by the US TV program Wild Kingdom, which I remember well, was the view that individuals behaved, sometimes or often, for the good of the species rather than for themselves as individuals of that species. However, every case that seemed to illustrate group selection behaviour could easily be interpreted otherwise. Take the case of ‘eusocial’ insects such as ants and bees, where most individuals don’t reproduce. This was seen as a prime case of group selection, where individuals sacrifice themselves for the sake of the highly reproductive queen. However, as evolutionary biologists George Williams and W D Hamilton later showed, eusocial insects have a unique genetic system in which they are all more or less equally ‘kin’, so it’s really another form of kin selection. This eusociality exists in some mammals too, such as mole rats.
Jacinta: The famous primatologist Sarah Hrdy dealt something of a death-blow to group selection in the seventies by observing that male langur monkeys in India commit infanticide with some regularity, and, more importantly, she worked out why. Langurs live in groups with one resident male to a bunch of females, with whom he makes babies. Meanwhile the other males tend to hang around in groups brooding instead of breeding, and infighting. Eventually, one of this male gang feels powerful enough to challenge the resident male. If he wins, he takes over the female group, and their babies. He knows they’re not his, and his time is short before he gets booted out by the next tough guy. Further, the females aren’t ovulating because they’re nursing their kids. The whole aim is to pass on his genes (this is individual rather than kin selection), so his best course of action is to kill the babs, get the females ovulating as quickly as possible, and impregnate them himself.
Canto: Yes, but it gets more complicated, because the females have just as much interest in passing on their genes as the male, and a bird in the hand is worth two in the bush…
Jacinta: Let me see, a babe in your arms is worth a thousand erections?
Canto: More or less precisely. So they fight the male to protect their infants, and can even go into ‘fake’ estrus, and mate with the male, fooling the dumb cluck into thinking he’s a daddy.
Jacinta: And since Hrdy’s work, infanticide of this kind has been documented in well over 100 species, even though it can sometimes threaten the species’ survival, as in the case of mountain gorillas. So much for group selection.
Canto: So now to kin selection. Here are some facts. If you have an identical twin your genome is identical with hers. If you have a full sibling you’re sharing 50% and with a half-sibling 25%. As you can see, the mathematics of genes and relatedness can be widened out to great degrees of complexity. And since this is all about passing on all, or most, or some of your genes, it means that ‘in countless species, whom you co-operate with, compete with, or mate with depends on their degree of relatedness to you’, to quote Sapolsky.
Jacinta: Yes, so here’s a term to introduce and then fairly promptly forget about: allomothering. This is when a mother of a newborn enlists the assistance of another female in the process of child-rearing. It’s a commonplace among primate species, but also occurs in many bird species. The mother herself benefits from an occasional rest, and the allomother, more often than not a younger relation such as the mother’s kid sister, gets to practice mothering.
Canto: So this is part of what is called ‘inclusive fitness’, where, in this case, the kid gets all-day mothering (if of varying quality) the kid sister gets to learn about mothering, thereby increasing her fitness when the time comes, and the mother gets a rest to recharge her batteries for future mothering. It’s hopefully win-win-win.
Jacinta: Yes, there are negatives and positives to altruistic behaviour, but according to Hamilton’s Rule, r.B > C, kin selection favours altruism when the reproductive success of relatives is greater than the cost to the altruistic individual.
Canto: To explain that rule, r equals degree of relatedness between the altruist and the beneficiary (aka coefficient of relatedness), B is the benefit (measured in offspring) to the recipient, and C is the cost to the altruist. What interests me most, though, about this kin stuff, is how other, dumb primates know who is their kin. Sapolsky describes experiments with wild vervet monkeys by Dorothy Cheney and Robert Seyfarth which show that if monkey A behaves badly to monkey B, this will adversely affect B’s behaviour towards A’s relatives, as well as B’s relatives’ behaviour to A, as well as B’s relatives’ behaviour to A’s relatives. How do they all know who those relatives are? Good question. The same researchers proved this recognition by playing a recording of a juvenile distress call to a group of monkeys hanging around. The female monkeys all looked at the mother of the owner of that distress call to see what she would do. And there were other experiments of the sort.
Jacinta: And even when we can’t prove knowledge of kin relations (kin recognition) among the studied animals, we find their actual behaviour tends always to conform to Hamilton’s Rule. Or almost always… In any case there are probably other cues, including odours, which may be unconsciously sensed, which might aid in inclusive fitness and also avoiding inbreeding.
Canto: Yes and It’s interesting how this closeness, this familiarity, breeds contempt in some ways. Among humans too. Well, maybe not contempt but we tend not to be sexually attracted to those we grow up with and, for example, take baths with as kids, whether or not they’re related to us. But I suppose that has nothing to do with kin selection. And yet…
Jacinta: And yet it’s more often than not siblings or kin that we have baths with. As kids. But getting back to odours, we have more detail about that, as described in Sapolski. Place a mouse in an enclosed space, then introduce two other mice, one unrelated to her, another a full sister from another litter, never encountered before. The mouse will hang out with the sister. This is called innate recognition, and it’s due to olfactory signatures. Pheromones. From proteins which come from genes in the major histocompatibility complex (MHC).
Canto: Histowhat?
Jacinta: Okay, you know histology is the study of bodily tissues, so think of the compatibility or otherwise of tissues that come into contact. Immunology. Recognising friend or foe, at the cellular, subcellular level. The MHC, this cluster of genes, kicks off the production of proteins which produce pheromones with a unique odour, and because your relatives have similar MHC genes, they’re treated as friends because they have a similar olfactory signature. Which doesn’t mean the other mouse in the enclosure is treated as a foe. It’s a mouse, after all. But other animals have their own olfactory signatures, and that’s another story.
Canto: And there are other forms of kin recognition. Get this – birds recognise their parents from the songs sung to them before they were hatched. Birds have distinctive songs, passed down from father to son, since its mostly the males that do the singing. And as you get to more complex species, such as primates – though maybe they’re not all as complex as some bird species – there might even be a bit of reasoning involved, or at least consciousness of what’s going on.
Jacinta: So that’s kin selection, but can’t we superior humans rise above that sort of thing? Australians marry Japanese, or have close friendships with Nigerians, at least sometimes.
Canto: Sometimes, and this is the point. Kinship selection is an important factor in shaping behaviour and relations, but it’s one of a multiple of factors, and they all have differential influences in different individuals. It’s just that such influences may go below the level of awareness, and being aware of the factors shaping our behaviour is always the key, if we want to understand ourselves and everyone else, human or non-human.
Jacinta: Good to stop there. As we’ve said, much of our understanding has come from reading Sapolsky’s Behave, because we’re old-fashioned types who still read books, but I’ve just discovered that there’s a whole series of lectures by Sapolsky, about 25, on human behaviour, which employs the same structure as the book (which is clearly based on the lectures), and is available on youtube here. So all that’s highly recommended, and we’ll be watching them.
References
R Sapolski, Behave: the biology of humans at our best and worst. Bodley Head, 2017
https://www.britannica.com/science/animal-behavior/Function#ref1043131
https://en.wikipedia.org/wiki/Kin_selection
https://en.wikipedia.org/wiki/Eusociality
modern humans are getting less modern, in unexpected places
Taken from the website of Science magazine
In recent years we’ve been almost overwhelmed by paleontological discoveries (and re-analyses of earlier discoveries), from giant worm jaws to a new subclass of cephalopod to a new semi-aquatic non-avian dinosaur to the oldest fossils yet found of that strange species, Homo sapiens.
I’ve decided to focus on the last example, for now. Homo sapiens fossils discovered at Jebel Irhoud in Morocco in the sixties, and long thought to have been some 40,000 years old, came under increasing ‘suspicion’ from palaeontologists, beginning in the eighties, due to various curious anomalies. More intensive searching at the Jebel Irhoud site recently has led to a wealth of discoveries, ‘including skull bones from five [human-like, though with a different brain-case, especially at the back] individuals who all died around the same time’. And thanks to the new thermoluminescence dating technique, which is applied to heated or burned substances (it’s a measure of accumulated radiation), a date of 300,000 years was calculated for the tools found near the fossils, and by association for the fossils themselves. This makes them over 100,000 years older than those found in Ethiopia. The Ethiopian fossil discoveries gave rise to the idea that ‘modern’ humans began life in a small region of East-Central Africa and gradually spread, but the revelation about the Moroccan fossils means a revision, or overturning, of that hypothesis.
You’ll notice I’ve put modern in skeptical quotes. It seems to me nobody will agree on what a modern human really is, or whether it’s decided entirely on anatomical or physiological features. If you found yourself suddenly transported to the days of Sargon and the Akkadian civilisation, only 4,500 years ago, you probably wouldn’t have the impression you were living among modern humans – depending on how prepared you were for the culture shock. Of course, paleontologists would have different measures for modernity – brain size, skeletal features and such – but these are necessarily imprecise given individual variation and the sparsity of really good fossils. And there’s also the matter of incremental, barely discernible change. For example, our 300,000-year-old Jebel Irhoud specimens are, perhaps, the oldest known modern human specimens, but it would be silly to argue that their parents weren’t just as modern – and what of their grandparents? And in this way we can go back another 10,000 years, or maybe 50,000, without seeing much difference. This has always been the most difficult thing to get my head around, not only for H sapiens but for any species. When does Australopithecus afarensis start/stop being Australopithecus afarensis? When did a chimp distinguish herself from a bonobo, and when did they both get differentiated from their predecessor? Are we taking hard and fast taxonomy too seriously? Maybe I’ll return to that some time…
Meanwhile, another recently revealed discovery has added to the ‘out of Africa’ confusion, which many thought was becoming less confused, with something like a consensus that H sapiens emerged from Africa between 70 and 100 thousand years ago and dispersed globally, with the oldest Australian human possibly dating back as far as 65,000 years.
The discovery of a human jawbone and teeth in Israel that date back nearly 200,000 years has messed up that simplifying story, and it’s only one of a number of finds that are making the experts get confused – and excited – again. The jawbone find, combined with sophisticated tools and weaponry, is solid evidence of H sapiens coming out of Africa much earlier, and perhaps on an irregular basis depending on climatic conditions and resources. Human teeth found in China, and human fossils in Sumatra, dating to at least 70,000 years ago, tend to confirm this hypothesis. Other fossil discoveries in Israel are complicating the picture. The Eastern Mediterranean seems to have been a crossroads where various early human species may have interacted.
These new discoveries appear to confound the genetic evidence that we’re all related to an out-of-Africa population that emerged well under 100,000 years ago, but it seems these early populations died out or returned to Africa.
Yet there are so many mysteries still to solve. What about the strange Denisovans? We have so little fossil evidence, yet enough to map almost the entire nuclear and mitochondrial genome – a testament to modern technology. Analysis of their mtDNA suggests that they migrated out of Africa much earlier than the modern humans above-mentioned, but later than H erectus. They apparently branched off from the human line 600,000 years ago, and from Neanderthals about 400,000 years ago. The fullness and fascinating richness of the Wikipedia article on the Denisovans, garnered from such minute fossil evidence, is a source of great wonder to me. The specimens (of four distinct Denisovans) were well preserved due to the icy temperatures in the Siberian cave, near the Mongolian-Chinese border, where they were found. The finger bone, dated to about 40,000 years BP (Before Present, a new designation to me, and a welcome one), has yielded both mitochondrial and nuclear DNA, which has shown the Denisovans to be distinct from both Neanderthals and modern humans, and that they share a common ancestor with Neanderthals. Other excavations of the cave show that it was inhabited at least 125,000 years ago. mtDNA analysis has apparently revealed that the three, H sapiens, Denisovans and Neanderthals, shared a common ancestor about 1 million years ago. I’m writing these facts, if they are facts, as I find them, while wondering what they mean, and especially how the evolutionary tree can be visualised, but it’s pretty difficult, especially when you consider interbreeding. Looks like I’ll have to write and do the research for half a dozen posts before I start to get it straight in my own head. Anyway, here’s one interesting chart I’ve found.
There are clearly more mystery hominids to be found, to fill out the complicating picture. And of course I’ve mentioned the genetics and genomics only in passing, but again it’s astonishing what they can find these days by comparing these genes with what we know of some modern human populations. For example, studies of the Denisovans genome found ‘a region around the EPAS1 gene that assists with adaptation to low oxygen levels at high altitude’, already known from analysis of modern Tibetan genes.
Hoping to keep myself up to date with all this, if I don’t get too distracted by the zillions of other fields of enquiry worth keeping up with…
References
https://en.wikipedia.org/wiki/Denisovan
All the excitation about Trump having tried to sack Mueller annoys me because it makes me – well, too excited. I have to learn to be patient. The Mueller enquiry will end when it does, and it’s sure to end dramatically. Still, I hunger for another indictment, or equivalent headline. One point worth worrying about though, is what happens when Trump goes? The whole administration should go, but that’s not what happens in the US. No snap elections, no double dissolution. Another weakness of the Presidential system, it seems to me. In the US, you vote for a personality, and that personality gets to build a team around him (it’s always been a bloke), whereas in most advanced western nations, the country’s leader has risen through the ranks of the team, much like the captain of a soccer team, who’s given the captain’s armband, not because she’s the best player – though she quite often is – but because she’s the most inspiring leader. If that captain falls afoul of the law, another competent team member can take on the job. In the case of the US Presidency, the team is tainted by the captain’s failings because he’s personally chosen the lot of them – in this case largely because of their political ignorance, which he regards as a positive.