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On Massimo Pigliucci on scientism: part 1 – what is science?

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Massimo Pigliucci, who seems like a nice enough bloke…

 

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

After new atheism: where now for the god debate? Talks by Marilynne Robinson, Roger Scruton and Jonathan Ree

Written by stewart henderson

May 23, 2019 at 11:50 am

kin selection – some fascinating stuff

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meerkats get together for ye olde family snap

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

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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://www.theguardian.com/science/2018/jan/25/oldest-known-human-fossil-outside-africa-discovered-in-israel

https://www.theatlantic.com/science/archive/2017/06/the-oldest-known-human-fossils-have-been-found-in-an-unusual-place/529452/

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.

 

Written by stewart henderson

January 29, 2018 at 10:31 pm

a bit more on cell cultures, cell mortality and patients’ rights

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Human connective tissue in culture, 500x. Image courtesy of Dr. Cecil Fox (photographer)/National Cancer Institute.

Canto: Well, we’ve followed up Meredith Wadman’s The vaccine race with Rebecca Skloot’s The immortal life of Henrietta Lacks, which intersects with Wadman’s book in describing cell cultures and their value in modern medicine and genetics. So are ready to talk about all this again?

Jacinta: Yes, this book tells a compelling history of the Lacks family as well as a story of the ethics around human cell cultures, based on the HeLa cell line taken from the cervix of Henrietta Lacks in 1951, shortly before she died of cervical cancer.

Canto: A very aggressive adenocarcinoma of the cervix, to be precise, though the tumour was misdiagnosed at the time.

Jacinta: Yes, her bodily state and her sufferings make for grim reading. And the cells were taken sans permission, in a pioneering era of almost no regulation and a great deal of dubious practice.

Canto: The wild west of cell and tissue culturology.

Jacinta: George Gey, the guy who ordered these cells to be taken, was a great pioneer in cancer and cell culture research, but he and others found it very difficult to keep human cells alive in vitro, so he was much surprised and delighted at his success with Henrietta’s tumour cells.

Canto: They were the first ever cells to live beyond the Hayflick limit, though that limit wasn’t spelt out by Hayflick until 1961.

Jacinta: And wasn’t accepted for decades after that. And the reason for their apparent immortality, a rare thing in untreated cells, was their cancerous nature. Human cancer cells contain an enzyme known as telomerase, which rebuilds the telomeres at the ends of chromosomes. Normally these telomeres, often described as like the protective caps at the ends of shoelaces, shorten and so become less protective with each cell division.

Canto: So if we could stop cancer cells from producing telomerase, you’d stop all that metastasising…

Jacinta: Sounds easy-peasy. And if we could introduce telomerase into non-cancerous cells we could all live forever.

Canto: Bet they haven’t thought of that one. So if this cell line was cancerous, how could they be of so much value? How could they be of any use at all, since the aim, I thought, was to produce ‘clean’ cells, like the WI-38 cells Hayflick produced ten years later? Remember how they had so many problems with monkey cells, which were full of viruses?

Jacinta: Well, forget viruses for the moment, the exciting thing about the HeLa cells was that they stayed alive and multiplied, which was rare, and so they could be experimented on in a variety of ways.

Canto: But did they use the cells for vaccines? The 1954 Salk polio vaccine was tested using these cells. How can you do this with cancerous cells?

Jacinta: Well it was the suitability of these cells for mass-production that made them ideal for test-driving the Salk vaccine, and of course their prolific nature was tied to their cancerous nature – Henrietta’s cancer seemed to be horribly fast-spreading, it was just about everywhere inside her at her death. Her cancer was caused by the human papilloma virus (HPV) and I’ve read that this may have had something to do with their prolific nature. She also had syphillis, likely contracted from her philandering husband, and this suppresses the immune system, allowing the cancer cells to multiply more rapidly. But even though they were cancer cells they shared many of the properties of normal cells, including the production of proteins and susceptibility to bacterial and especially viral infections. Of course you would never inject HeLa cells into humans, but their malignancy is an advantage in that you get the results of say, viral infection of cells as they reproduce, much more quickly than with normal cells, because of their reproductive rate. It seems old George Gey hit the jackpot with them, though he never made any more money out of them than the Lackses did.

Canto: They initially used rhesus monkey cells to test their antibody levels in response to Salk’s killed polio virus, but they were too hard to get and too expensive, and the HeLa cells were an excellent alternative because they were easily infected by the virus… and they reproduced with unprecedented alacrity.

The malignancy of immortality (or vice versa). A HeLa cell splitting into two new cells. The green spots are chromosomes. Courtesy Paul D. Andrews)

Jacinta: Yes, that’s to say, they readily produced antibodies, and so could be experimented on to produce the level of antibodies to create immunity. But growing cell cultures in vitro and maintaining them in a viable state, that’s been a decades-long learning process. Tissue culture these days is big business, which has led to the murky ethical questions about tissue ownership that Skloot refers to at the end of her book.

Canto: Yes but I for one am quite clear about that issue. I’m more than happy for researchers to use any tissue that comes from, say, a biopsy done on me. Is that tissue mine, when it’s removed from my body?

Jacinta: Well, is it? Think of locks of hair kept from a loved one – something that happens a few times in Skloot’s book. Wouldn’t you be moved by a lock of hair that you knew came from someone you loved but who was no longer around? Wouldn’t you feel you had hold of a part of her? Not just a memory of her?

Canto: Interesting. I think I’d be in two minds about it. I’d think, yes, this is her hair, a small part of her, and that would bring all the emotion of identity with it. But then, what I know about science and cells tells me this is just hair, it’s not what makes her her. It’s nowhere near it. Our hair is discarded all the time.

Jacinta: If you had some of her brain cells? Or heart tissue haha?

Canto: Nothing but ultra-ultra minuscule parts of the whole. And essentially meaningless when disconnected from that whole. But this misses the point that the value of this tissue for research outweighs by far, to me at any rate, the sentimental value that you’re talking about.

Jacinta: But for some people, and some cultures, the intactness of the human entity, after death say, is of deep-rooted significance. Are you not prepared to respect that?

Canto: But we slough off our trillions of cells all the time. Even as a kid I was told we replace our cells every seven years. Of course it’s much more varied and complicated than that, but the general point of constant renewal is true.

Jacinta: Yes but they’re your cells, with your DNA in them, nobody else’s.

Canto: Well people are prepared to be operated on, which inevitably kills or removes cells, and in doing so they give themselves up to experts in healing their bodies and often saving their lives, so it would seem to me pretty mean-spirited not to allow those experts to make use of what’s removed, which is of no obvious use to them.

Jacinta: I think you have a good argument there, but what if these mad scientists use your cells for some nefarious purpose?

Canto: Well, call me a trusting soul, but why would they do that? And what nefarious purpose could they use them for?

Jacinta: Well it mightn’t even be nefarious. With the modern commercialisation of cell and gene technology, they might find your tissue perfect for developing something patentable, out of which they make shitloads of money while preventing independent research on the tissue, so using your cells in a way that you might strongly disapprove of. But you wouldn’t have the slightest say, as things stand today. Rebecca Skloot describes examples of this kind in the Afterword to her book. There’s been a raging debate about commercialisation and gene patents and patients’ rights for some time now in the USA, and no doubt elsewhere, with scientists and other stakeholders ranged along the spectrum. In fact, these are the last words of Skloot’s book, published in 2010:

2009: More than 150,000 scientists join the American Civil Liberties Union and breast cancer patients in suing Myriad Genetics over its breast-cancer gene patents. The suit claims that the practice of gene patenting violates patent law and has inhibited scientific research.

Canto: Right. As her investigations reveal, it’s not just about patients wanting a share of the loot from research on their cells, and so using the courts to bog everything down and hinder that research, it’s often about researchers themselves wanting to cash in, and patients joining with other researchers to try to free up the system for the common good. So how’s the Myriad Genetics case going, and how’s the situation regarding patient rights in this field, several years on?References

Jacinta: Well in the case of Myriad, it was all highly complex and litigious, with suits and countersuits, which the company mostly lost, in particular in a landmark (and unanimous) Supreme Court decision of 2013, in which they found that ‘merely isolating genes that are found in nature [in this case the BRCA-1 and BRCA-2 genes] does not make them patentable’. But of course this wasn’t so much about patients’ rights in the material that was once part of their bodies. It’s not all about money – though much of it is, and if you don’t want the money landing in lawyers’ pockets, the best thing is to have clear guidelines, disclosure, and fully developed and complex consent procedures. My impression from doing a fairly shallow dive on the issues is that we’re a long way from sorting this out, in an increasingly complex and lucrative field. Our own federal government’s NHMRC has a booklet out, available on PDF, called ‘Ethics and the exchange and commercialisation of products derived from human tissue: background and issues’, which is already six years old, but I don’t see anything in the legislative pipeline.

Canto: Looks like an issue to be followed up, if we have the stomach for it.

Jacinta: It pays to be informed, that’s one obvious take-away from all this.

References
Rebecca Skloot, The immortal life of Henrietta Lacks, 2010
Meredith Wadman, The vaccine race, 2017

Written by stewart henderson

July 3, 2017 at 12:22 pm

how evolution was proved to be true

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The origin of species is a natural phenomenon

Jean-Baptiste Lamarck

The origin of species is an object of inquiry

Charles Darwin

The origin of species is an object of experimental investigation

Hugo de Vries

(quoted in The Gene: an intimate history, by Siddhartha Mukherjee)

Gregor Mendel

I’ve recently read Siddhartha Mukherjee’s monumental book The Gene: an intimate history, a work of literature as well as science, and I don’t know quite where to start with its explorations and insights, but since, as a teacher to international students some of whom come from Arabic countries, I’m occasionally faced with disbelief regarding the Darwin-Wallace theory of natural selection from random variation (usually in some such form as ‘you don’t really believe we come from monkeys do you?’), I think it might be interesting, and useful for me, to trace the connections, in time and ideas, between that theory and the discovery of genes that the theory essentially led to.

One of the problems for Darwin’s theory, as first set down, was how variations could be fixed in subsequent generations. And of course another problem was – how could a variation occur in the first place? How were traits inherited, whether they varied from the parent or not? As Mukherjee points out, heredity needed to be both regular and irregular for the theory to work.

There were few clues in Darwin’s day about inheritance and mutation. Apart from realising that it must have something to do with reproduction, Darwin himself could only half-heartedly suggest an unoriginal notion of blending inheritance, while also leaning at times towards Lamarckian inheritance of acquired characteristics – which he at other times scoffed at.

Mukherjee argues here that Darwin’s weakness was impracticality: he was no experimenter, though a keen observer. The trouble was that no amount of observation, in Darwin’s day, would uncover genes. Even Mendel was unable to do that, at least not in the modern DNA sense. But in any case Darwin lacked Mendel’s experimental genius. Still, he did his best to develop a hypothesis of inheritance, knowing it was crucial to his overall theory. He called it pangenesis. It involved the idea of ‘gemmules’ inhabiting every cell of an organism’s body and somehow shaping the varieties of organs, tissues, bones and the like, and then specimens of these varied gemmules were collected into the germ cells to produce ‘mixed’ offspring, with gemmules from each partner. Darwin describes it rather vaguely in his book The Variation of Animals and Plants under Domestication, published in 1868:

They [the gemmules] are collected from all parts of the system to constitute the sexual elements, and their development in the next generation forms the new being; but they are likewise capable of transmission in a dormant state to future generations and may then be developed.

Darwin himself admitted his hypothesis to be ‘rash and crude’, and it was effectively demolished by a very smart Scotsman, Fleeming Jenkin, who pointed out that a trait would be diluted away by successive unions with those who didn’t have it (Jenkin gave as an example the trait of whiteness, i.e. having ‘white gemmules’, but a better example would be that of blue eyes). With an intermingling of sexual unions, specific traits would be blended over time into a kind of uniform grey, like paint pigments (think of Blue Mink’s hit song ‘Melting Pot’).

Darwin was aware of and much troubled by Jenkin’s critique, but he (and the scientific world) wasn’t aware that a paper published in 1866 had provided the solution – though he came tantalisingly close to that awareness. The paper, ‘Experiments in Plant Hybridisation’, by Gregor Mendel, reported carefully controlled experiments in the breeding of pea plants. First Mendel isolated ‘true-bred’ plants, noting seven true-bred traits, each of which had two variants (smooth or wrinkled seeds; yellow or green seeds; white or violet coloured flowers; flowers at the tip or at the branches; green or yellow pods; smooth or crumpled pods; tall or short plants). These variants of a particular trait are now known as alleles. 

Next, he began a whole series of painstaking experiments in cross-breeding. He wanted to know what would happen if, say, a green-podded plant was crossed with a yellow-podded one, or if a short plant was crossed with a tall one. Would they blend into an intermediate colour or height, or would one dominate? He was well aware that this was a key question for ‘the history of the evolution of organic forms’, as he put it.

He experimented in this way for some eight years, with thousands of crosses and crosses of crosses, and the more the crosses multiplied, the more clearly he found patterns emerging. The first pattern was clear – there was no blending. With each crossing of true-bred variants, only one variant appeared in the offspring – only tall plants, only round peas and so on. Mendel named them as dominant traits, and the non-appearing ones as recessive. This was already a monumental result, blowing away the blending hypothesis, but as always, the discovery raised as many questions as answers. What had happened to the recessive traits, and why were some traits recessive and others dominant?

Further experimentation revealed that disappeared traits could reappear in toto in further cross-breedings. Mendel had to carefully analyse the relations between different recessive and dominant traits as they were cross-bred in order to construct a mathematical model of the different ‘indivisible, independent particles of information’ and their interactions.

Although Mendel was alert to the importance of his work, he was spectacularly unsuccessful in alerting the biological community to this fact, due partly to his obscurity as a researcher, and partly to the underwhelming style of his landmark paper. Meanwhile others were aware of the centrality of inheritance to Darwin’s evolutionary theory. The German embryologist August Weismann added another nail to the coffin of the ‘gemmule’ hypothesis in 1883, a year after Darwin’s death, by showing that mice with surgically removed tails – thus having their ‘tail gemmules’ removed – never produced tail-less offspring. Weismann presented his own hypothesis, that hereditary information was always and only passed down vertically through the germ-line, that’s to say, through sperm and egg cells. But how could this be so? What was the nature of the information passed down, information that could contain stability and change at the same time?

The Dutch botanist Hugo de Vries, inspired by a meeting with Darwin himself not long before the latter’s death, was possessed by these questions and, though Mendel was completely unknown to him, he too looked for the answer through plant hybridisation, though less systematically and without the good fortune of hitting on true-breeding pea plants as his subjects. However, he gradually became aware of the particulate nature of hereditary information, with these particles (he called them ‘pangenes’, in deference to Darwin’s ‘pangenesis’), passing down information intact through the germ-line. Sperm and egg contributed equally, with no blending. He reported his findings in a paper entitled Hereditary monstrosities in 1897, and continued his work, hoping to develop a more detailed picture of the hereditary process. So imagine his surprise when in 1900 a colleague sent de Vries a paper he’d unearthed, written by ‘a certain Mendel’ from the 1860s, which displayed a clearer understanding of the hereditary process than anyone had so far managed. His response was to rush his own most recent work into press without mentioning Mendel. However, two other botanists, both as it happened working with pea hybrids, also stumbled on Mendel’s work at the same time. Thus, in a three-month period in 1900, three leading botanists wrote papers highly indebted to Mendel after more than three decades of profound silence.

Hugo de Vries

The next step of course, was to move beyond Mendel. De Vries, who soon corrected his unfair treatment of his predecessor, sought to answer the question ‘How do variants arise in the first place?’ He soon found the answer, and another solid proof of Darwin’s natural selection. The ‘random variation’ from which nature selected, according to the theory, could be replaced by a term of de Vries’ coinage, ‘mutation’. The Dutchman had collected many thousands of seeds from a wild primrose patch during his country rambles, which he planted in his garden. He identified some some 800 new variants, many of them strikingly original. These random ‘spontaneous mutants’, he realised, could be combined with natural selection to create the engine of evolution, the variety of all living things. And key to this variety wasn’t the living organisms themselves but their units of inheritance, units which either benefitted or handicapped their offspring under particular conditions of nature.

The era of genetics had begun. The tough-minded English biologist William Bateson became transfixed on reading a later paper of de Vries, citing Mendel, and henceforth became ‘Mendel’s bulldog’. In 1905 he coined the word ‘genetics’ for the study of heredity and variation, and successfully promoted that study at his home base, Cambridge. And just as Darwin’s idea of random variation sparked a search for the source of that variation, the idea of genetics and those particles of information known as ‘genes’ led to a worldwide explosion of research and inquiry into the nature of genes and how they worked – chromosomes, haploid and diploid cells, DNA, RNA, gene expression, genomics, the whole damn thing. We now see natural selection operating everywhere we’re prepared to look, as well as the principles of ‘artificial’ or human selection, in almost all the food we eat, the pets we fondle, and the superbugs we try so desperately to contain or eradicate. But of course there’s so much more to learn….

William Bateson

Written by stewart henderson

June 14, 2017 at 5:42 pm

touching on the complex causes of male violence

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gangs-1

A bout of illness and a general sense of despair about blogging has prevented me from posting here for a while. For my health and well-being I’ll try to get back on track. So here’s a brief post on my hobbyhorse of the moment.

It surprises me that people could try to argue with me about the violence of men compared to women, trying to explain it away in terms of physical size – I mean, really? And then, when this doesn’t fly, they point to individuals of established combativeness, the Iron Lady, Golda Meir, and why not mention Boadicea, or [place name of fave female serial killer here]?
And it really demoralises me when this argumentative cuss is a woman. I mean I love a feisty female but really…
It reminds me of a scenario from my not-so-youth, when I briefly hung out with a perverse young lass who insisted with unassailable feistiness that men were clearly more intelligent than women (by and large, presumably). It certainly made be wonder at how intelligence could be turned against itself. But was it intelligence, or something else?

But let’s get back to reality. Men are more violent than women in every country and every culture on the planet. This is a statistical fact, not a categorical, individual claim. Of course there are violent women and much less violent men. That isn’t the point. The point is that you cannot sheet this home to sexual dimorphism. Two examples will suffice. First, look at death and injury by road accident in the west – in countries where both men and women are permitted to drive. The number of males killed in road accidents is considerably higher than females in every western country. In Australia males are almost two and a half times more likely to die this way than females, and in some countries it’s more, but it’s everywhere at least double. The WHO has a fact sheet On this, updated in November 2016:

From a young age, males are more likely to be involved in road traffic crashes than females. About three-quarters (73%) of all road traffic deaths occur among men. Among young drivers, young males under the age of 25 years are almost 3 times as likely to be killed in a car crash as young females.

The second example is youth gangs, including bikie gangs. These are, obviously, predominantly male, their purpose is usually to ‘display manhood’ in some more or less brutal way, and, again obviously, they can’t be explained away in terms of size difference. Other causes need to be considered and studied, and of course, they have been. Some of these causes are outlined in Konner’s book, but I can’t detail them here because I’ve lent the book out (grrr). An interesting starting point for thinking about the social causes of male violence is found in a short essay by Jesse Prinz here. Prinz largely agrees with Konner on the role of agricultural society in sharpening the male-female division in favour of males, but I think he oversimplifies the differences in his tendency to apply social explanations, and he says nothing about gene expression and hormonal factors, which Konnor goes into in great detail. It seems to me that Prinz’s line of reasoning would not be able to account for the reckless, life-threatening behaviour of young male drivers, for example. While there is clearly something social going on there, I would contend that something biological is also going on. Or something in the biological-social nexus, if you will. Clearly, it’s a very complex matter, and if we can uncover hormonal or neurotransmissional causes, that doesn’t rule out social factors playing a regulatory role in those causes. Social evolution, we’re finding, can change biology much more quickly than previously thought.

Written by stewart henderson

November 6, 2016 at 11:59 am

bonobos and us – lessons to be learnt

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image

Let’s be sexy about this

Bonobos separated from chimps maybe less than a million years ago, according to some pundits. We haven’t yet been able to determine a more precise date for the split. So which species has changed more? Have chimps become more aggressive or have bonobos become more caring? Is there any way of finding out?
It’s not just about genes its about their expression. It will take some time to work all that out. Brain studies too will help, as we move towards scanning and exploring brains more effectively and less invasively.
But surely we seek not just to understand the bonobo world but to change our own. Who wouldn’t want a world that was less violent, less exclusionary in terms of sex, more caring and sharing, without any loss of the dynamism and questing that has taken us to to the very brink of iphone7?
That last remark will date very quickly… Nah, I’ll leave it in.
So we can learn lessons, and of course we’re already on that path. Advanced societies, if that’s not too presumptuous a term, are less patriarchal than they’ve ever been, without losing any of their dynamism. On the contrary, it can easily be seen that the most male-supremacist societies in the world are also the most violent, the most repressive and the most backward. Some of those societies, as we know, have their backwardness masked by the fact that they have a commodity, oil, that the world is still addicted to, which has made the society so rich that their citizens don’t even have to pay tax. The rest of the world is supporting tyrannical regimes, which won’t change as long as they feel well-fed and secure. Not that I’d wish starvation and insecurity on anyone, but as Roland Barthes once said at one of his packed lectures, the people standing at the back who can’t hear properly and have sore feet must be wondering why they’re here.
Maybe a bit of discomfort, in the form of completely shifting away from fossil fuels for our energy needs haha, might bring certain Middle Eastern countries to a more serious questioning of their patriarchal delusions? Without their currently-valuable resource, they might wake to the fact that they need to become smarter. The women in those countries, so effective on occasion in forming coalitions to defend their inferior place in society, might be encouraged to use their collective power in more diverse ways. That could be how things socially evolve there.
Meanwhile in the west, the lesson of the bonobos would seem to be coalitions and sex. We’ve certainly arrived at an era where sexual dimorphism is irrelevant, except where women are isolated, for example in domestic situations. The same isolation also poses a threat to children. The bonobo example of coalitions and togetherness and sharing of responsibilities, and sexual favours (something we’re a long way from emulating, with our jealousies and petty rivalries) should be the way forward for us. Hopefully the future will see a further erosion of the nuclear family and a greater diversity of child-rearing environments, where single-parent families are far less isolated than they are today, and males want to help and support and teach children because they are children, not because they are their children…

Written by stewart henderson

September 10, 2016 at 6:54 pm