When I first heard about epigenetics, I hated it. I still do, in fact, but I am slowly beginning to accept the fact that epigenetics is a fact. And it’s a terrible fact, like all facts that force one to radically change one’s long-held ideas.
In the 19th century everyone knew about inheritance, but nobody knew about genes. Two similar theories of evolution were proposed, one in 1809 by Lamarck, and 50 years later a more complete one by Darwin. Both men proposed that species can change their characteristics over time and that such changes can even produce new species, and both saw the role of the environment as critical to this process. Lamarck’s theory was that when creatures experienced environmental changes to their characteristics, these changes could be inherited, resulting in evolution of the population.
Darwin’s theory saw evolution proceeding in two major steps. First there were heritable changes, and then environmental conditions selected which organisms would survive and reproduce based on the phenotypes produced by these inherited changes.
The 20th century saw the flowering of Mendelian inheritance into a major science. The concept of the gene – the hypothetical inheritance particle – was substantiated by the discovery of the structure and function of DNA. Darwin’s theory was confirmed, Lamarckian ideas were utterly rejected – both on theoretical and observational grounds – and neo-Darwinism was born.
And that’s how things have stood for the past 60 years or so. The inheritance of acquired characteristics, as Lamarkian evolution has been summarized, was dismissed as nonsense, with no evidence and lots of counterevidence.
Until recently. Don’t you love science? It’s never boring. I first heard about epigenetics when I was researching the environmental causes of cancer. The idea was that in some circumstances, certain parts of the DNA molecule are modified with methyl groups that change the expression (usually by repression) of a gene. This modification of gene function can act like a mutation, since if a gene is not expressed, it’s just as if it had undergone a mutation. By itself, these findings were not terribly dramatic, because such methylation and its effects could not possibly be inherited, so I (and everyone else) thought of these epigenetic changes (called marks) as having no impact on basic Darwinian theory.
Oops. Over the past decade, it has become clear that sometimes these epigenetic changes, due to various exposures or environmental influences, can in fact be inherited, even after the exposure is over. At first it seemed that this only happened for a few generations. But no. That would be too easy. It now appears pretty likely that some epigenetic effects are long-lasting, perhaps permanent, just like a mutation in the DNA sequence. The crucial difference is that mutations are very rare, accumulate slowly, and are random, while epigenetic effects can be very rapid, much more frequent, and targeted to specific genes.
Welcome back, M. Lamarck. Having been educated for over four decades that Lamarckian evolution is a nonsensical, utterly wrong idea, I was not happy. But that’s science. Physicists have gone through this sort of thing routinely in the past century or so, and now it’s the turn of biologists.
The implications of long-term inheritance of epigenetic alteration of genomes are staggering. If epigenetics is a real mechanism of evolution, as real as the neo-Darwinian mechanism of mutation and natural selection, then everything in biology changes. The good news is that a lot of tough question might be answered, such as how phenotypic innovations can lead to major and rapid appearance of new biological features, without needing the very slow, laborious process of mutation accumulation (allelic variation) followed by selection. The bad news is that almost everything we thought we knew about evolution must now be re-thought.
As in all such paradigm shifts, traditional Darwinian genetic evolution is not disproven; it has been modified to include a host of new mechanisms (epigenetics being a major example, but not the only one). Lamarck is back, with his own molecular mechanism of epigenetics to be joined with Darwin’s genetic mechanism. The theoretical and predictive implications of this merger are both incredibly complex and very exciting. I propose that the new theory of evolution combining inherited germline mutations and inherited epigenetic marks be called Darmarckian evolution. And to all my colleagues who share my horror at such a heretical vision of how biology actually works, I can only say (as I have had to say to myself), “It’s science – deal with it”.
The Book of Works 
It’s only in retrospect that it’s clear that what I was taught at school – that Lamarckism was disproven by the fact that cutting of the tails of mice didn’t lead to tailless offspring – was a pretty inadequate rebuttal.
Lamarck actually had two theories of evolution – acquired characteristics was his explanation for variation, but he believed the general pattern was a lawlike orthogenesis. Maybe that too will come in from the cold before long!
Yes. That’s a major theme of Denton’s book quoting Owen a lot. I hope all is well, Jon. I will be sending you an email soon.
Forgive my most likely, very naive question. I didn’t learn evolution at school (perhaps becasue I didn’t go on to do Biology O Level). I think I understand it however on a very basic non-technical level.
I just read your article which was a little confusing to me because I haven’t heard some of those terms you used. However, from what I could understand, this would seem to make a lot of sense. The very long gradual change has never made much sense to me on some levels (remembering of course that I have not studied science, only know stuff I’ve read).
It seems to me that whole populations of people, creatures etc would have been/be quite quickly wiped out, if there were not, at least on occasion, a more rapid ‘evolution’ or adaptation.
On the other hand I have always understood (maybe wrongly) that, for example, people in Africa are dark-skinned because of the sun..and people in , say Scandinavia, are light-skinned with fair hair, presumably because of lack of sun, also less daylight, at least in winter months. However, what puzzles me is that dark-skinned people in western European countries still remain dark-skinned..and so do their children (provided the offspring are born of similar parents, grandparents etc). One would think that, over time, if they lived in Scandinavia for instance, that according to adaptation, the descendents would eventually become light-skinned. Or hasn’t there been enough time yet for them to turn into, as it were, more Scandinavian-looking people? And vice-versa, of course, light-skinned people living in Africa, for example.
Sorry my question is not very well phrased, but I don’t know the best way to explain what I mean
Hi P Young
By your O levels I recognise you as a compatriot! Just a quick comment on dark skin.
You might remember the reconstruction of Cheddar Man a month or two ago, showing that Brits in the early Mesolithic, c10,000 BC were pretty black (but also blue-eyed). Presumably his ancestors had weathered the whole Ice Age in Europe quite successfully with their dark skin. The next wave of immigrants, from warmer climes (if memory serves) were light skinned, and it would therefore seem quite possible that the mutations that led to that change were near-neutral, ie that there’s no massive adaptive advantage one way or the other, regardless of climate.
Which leads to the question, why did Lamarckians say that dark skin was an inherited suntan, and the Darwinian generations since that accidental mutations favour dark races in hot countries and light skin in cold ones?
The answer seems to be that those explanations fit the favoured theories, rather than that anyone actually did experiments to measure either darkness against amount of sun in native populations, or even whether skin colour gives a survival edge in different climates. As far as I know, that work has still not been done.
Thank you for your reply. I expect it would be rather difficult to do actual experiments as to whether or not pigmentaion would adapt/evolve over time.
Something I find very interesting is that there is a group of people living very high up somewhere (can’t remember where, saw a documentary). The air is very rarefied, so that people who weren’t born and brought up there found it harder to function. However, those who lived there had some kind of adaptation, from birth I believe, so that they had no problem walking, running etc. I can’t remember all the details unfortunately..but I did wonder whether it was something that naturally developed during gestation, or whether it was something passed down genetically (having already become adapted, so to speak). I’d love to know the answer. It makes me wonder if supposing someone from another country, went there to live and became pregnant, whether the foetus would develop in the womb the extra oxygen-processing ‘equipment’ for want of a better word, due to being up there from conception..or whether they would be born exactly the same as the mother not born there.
P Young
For once, altitude adaptation appears to be a straightforward example of genetic adaptation by natural selection. In the various cases – Ethiopian highlands, Himalayas, Andes – a couple of genes (different in each case) have mutated in a way that favours the oxygen-carrying capacity of the blood. Infant mortality is lower in those having it, so they survive and breed, and so in time become the whole population.
In the case of the Sherpas, it’s apparently the fastest example of selection known in humans, occurring in just 3,000 years – but that’s partly because it’s a small population, where selection works better.
So most foreigners trying to have babies up in the high mountains wouldn’t do well – unless by chance they carried an unusual gene or two. Of course, this is all different from the acclimatisation due to physiology that we all show after a few days or weeks at altitude – presumably some better than others, again because of what genes we happen to have. We lose that when we return to low-altitude life. If there’s any epigenetic effect it hasn’t been recorded yet!
Jon Garvey:- Thank you again for your further reply re high altitude living.
It would be great if they could do more research on this kind of thing. Very interesting.
I actually have lots more questions about related things…but I won’t pester you with them, especially as it would take quite a while for me to write them out..and no doubt, quite a while for you to answer them!
The problem is, if one hasn’t studied science, is that one can read a simple book or Google stuff for basic explanations…but there are still too many unanswered questions…but if one goes into more complex books or websites, then they are TOO complicated and one ends up having to look up what a thousand different technical or scientific words mean, by which time, one has forgotten the original question!
At school, I always wanted to go deeper than what they were teaching…for example in chemistry, we would bung a couple of chemicals together which made a bright flash or whatever…but I though what’s the use of that? Where do these chemicals come from..how do we extract them? To what use can this information be put? Etc etc. In physics we did ‘ripple tanks’. Boring as anything. I thought well, one can see the difference in frequencies etc just by general everyday observation, like when one chucks a stone in a pond, depending on different factors it will cause different heights and lengths of waves. Again, I wanted to know what application this had. Didn’t need to do ripple tanks. If it was to help us get the concept of different things like radio waves, light etc, then it didn’t of itself, help. And in the first year, we did ‘fulcrums’…I thought, well we learnt all about that years ago, playing on seesaws.
To my mind, my husband did much better science/technical stuff at school. His class built a go-kart, so whilst doing that, they saw the practical application of all kinds of things…maths, stress (metal), metalwork, design and so on and so on. And when something didn’t work, they had to figure it out so that it did work.
Exciting frontiers in the biological sciences; maybe I should study biology now that I’m back in school. Thanks for this post, Sy. I like that you pointed out, as you did when you addressed these new developments in your ASA talk during the summer of 2016, that epigenetics doesn’t negate Darwinian evolution or make biological evolution “a theory in crisis”. Sounds like there’s just more to the story than was originally thought. Would you say that’s a correct assessment?
Peace, my friend. Hope you’re doing great.
Ethan, yes that is a perfect assessment. In Biology it seems that there is always more to the story than was originally thought. Thanks for asking, I am doing quite well. Stay tuned for some good news to be posted here.
P Young
We never made go-karts in physics, sadly – my most positive practical science at school was, unfortunately, to accidentally poison a lawn full of worms with formalin, trying to get them to surface. The caretaker was a bit upset about the lawn too. Somehow, I struggled through to an A and S level zoology and Cambridge University.
But hang around Sy’s blog for awhile, and you’ll learn some cutting edge biology from the guy doing it, who explains it brillaintly. A rare privilege (just send the cheque in the post, Sy!).
That is funny about the worms! Would have been a lot easier just to have dug them up!
I do like seeing what one can DO with things…I was always lousy at maths (so it wouldn’t have been much good my continuing with physics anyhow). But I always got on quite well with geometry..I loved how in the first year at secondary school they showed us how to find the height of a tree with a rubber and protractor. I thought that was ace! No complicated technology either. (Not that I’ve ever had to find the height of something in real life…but one never knows, it could come in handy!)
What! And damage the school lawn?
Haha! I was only jesting! I bet you anything though that science of some form or another comes into spades…think about the right temperature for extracting the metal and heating it so that it is the right hardness etc. What about ergonomics? (I think that’s the right word). A spade isn’t necessarily a simple thing. Also, think abou the human body, the stresses and strains digging can cause… Still, I suppose all that would probably come under metalwork, technology and health, rather than pure science LOL
And anyway, this was science – formalin is science, spades are just work.
Wait, I thought I had paid in advance!! Thanks Jon
How is all this supposed to work with population genetics? For example, Shapiro’s stuff about bacteria mutation rates increasing due to environmental stress…epigenetics…etc…why aren’t creationists saying that these things make population genetics impossible? I’m assuming I’m missing something because it doesn’t seem like Noble and Shapiro or even Perry Marshall (who accepts the genetic evidence that the human race doesn’t go back to a single couple) want to do away with population genetics.
Would they just say that the mutation rate being calculated is not the rate of “copying errors” but of something like directed substitutions? But assuming Shapiro is right, how can we know that these substitutions didn’t increase dramatically due to environmental pressures? How are mathemtical models possible?
Once again, I am just trying to understand. I’ve found Venema’s stuff on population genetics extremely convincing (and I don’t think Richard Buggs’ work really contradicts it, as the latest blog on BioLogos also says), but how is it supposed to fit together with all these other marvelous mechanisms?
-Mark