‘All domestic animals and plants are genetically modified already’

There is an argument among people who, like yours truly, support (or at least are not in principle against) applications of genetic modification in plant and animal breeding that ‘all domestic animals and plants are genetically modified already’ because of domestication and breeding. See for example Food Evolution or this little video from Sonal Katyal.

This is true in one sense, but it’s not very helpful, for two reasons.

First, it makes it look as if the safety and efficacy of genome editing turns on a definition. I don’t know what the people who pull out this idea in discussion expect that the response will be — that the people who worry about genetic modification as some kind of threat will go ‘oh, that was a clever turn of phrase; I guess it’s no problem then’. Again, I think the honest thing to say is that genetic modification (be it mutagenesis, transgenetics, or genome editing) is a different thing than classic breeding, but that it’s still okay.

Second, I also fear that it promotes the misunderstanding that selective breeding is somehow outdated and unimportant. This video is an example (and I don’t mean to bash on the video; I think what’s said in it is true, but not the whole story). Yes, genome editing allows us to introduce certain genetic changes precisely and independently of the surrounding region. This is as opposed to introducing a certain variant by crossing, when other undesired genetic variants will follow along. However, we need to know what to edit and what to put instead, so until knowledge of causative variants is near perfect (spoiler: never), selection will still play a role.

Genome editing in EU law

The European Court of Justice recently produced a judgement (Case C-528/16) that means that genome edited organisms will be regarded as genetically modified and subject to the EU directive 2001/18 about genetically modified organisms, which is bad news for anyone who wants to use genome editing to do anything with plant or animal breeding in Europe.

The judgement is in legalese, but I actually found it more clear and readable than the press coverage about it. The court does not seem conceptually confused: it knows what genome editing is, and makes reasonable distinctions. It’s just that it’s bound by the 2001 directive, and if we want genome editing to be useful, we need something better than that.

First, let’s talk about what ‘genetic modification’, ‘transgenics’, ‘mutagenesis’, and ‘genome editing’ are. This is how I understand the terms.

  • A genetically modified organism, the directive says, is ‘an organism, with the exception of human beings, in which the genetic material has been altered in a way that does not occur naturally by mating and/or natural recombination’. The directive goes on to clarify with some examples that count as genetic modification, and some that don’t, including in vitro fertilisation as well as bacterial and viral processes of horizontal gene transfer. As far as I can tell, this is sensible. The definition isn’t unassailable, of course, because a lot hinges on what counts as a natural process, but no definition in biology ever is.
  • Transgenics are organisms that have had new DNA sequences introduced into them for example from a different species. As such, their DNA is different in a way that is very unlikely to happen by spontaneous mutation. For technical reasons, this kind of genetic modification, even if it may seem more dramatic than changing a few basepairs, is easier to achieve than genome editing. This the old, ‘classic’, genetic modification that the directive was written to deal with.
  • Mutagenesis is when you do something to an organism to change the rate of spontaneous mutation, e.g. treat it with some mutagenic chemical or radiation. With mutagenesis, you don’t control what change will happen (but you may be able to affect the probability of causing a certain type of mutation, because mutagens have different properties).
  • Finally, genome editing means changing a genetic variant into another. These are changes that could probably be introduced by mutagenesis or crossing, but they can be made more quickly and precisely with editing techniques. This is what people often envisage when we talk about using Crispr/Cas9 in breeding or medicine.

On these definitions, the Crispr/Cas9 (and related systems) can be used to do either transgenics, mutagenesis or editing. You could use it for mutagenesis to generate targeted cuts, and let the cell repair by non-homologous end joining, which introduces deletions or rearrangements. This is how Crispr/Cas9 is used in a lot of molecular biology research, to knock out genes by directing disruptive mutations to them. You could also use it to make transgenics by introducing a foreign DNA sequence. For example, this is what happens when Crispr/Cas9 is used to create artificial gene drive systems. Or, you could edit by replacing alleles with other naturally occurring alleles.

Looking back at what is in the directive, it defines genetically modified organisms, and then it goes on to make a few exceptions — means of genetic modification that are exempted from the directive because they’re considered safe and accepted. The top one is mutagenesis, which was already old hat in 2001. And that takes us to the main question that the judgment answers: Should genome editing methods be slotted in there, with chemical and radiation mutagenesis, which are exempt from the directive even if they’re actually a kind of genetic modification, or should they be subject to the full regulatory weight of the directive, like transgenics? Unfortunately, the court found the latter. They write:

[T]he precautionary principle was taken into account in the drafting of the directive and must also be taken into account in its implementation. … In those circumstances, Article 3(1) of Directive 2001/18, read in conjunction with point 1 of Annex I B to that directive [these passages are where the exemption happens — MJ], cannot be interpreted as excluding, from the scope of the directive, organisms obtained by means of new techniques/methods of mutagenesis which have appeared or have been mostly developed since Directive 2001/18 was adopted. Such an interpretation would fail to have regard to the intention of the EU legislature … to exclude from the scope of the directive only organisms obtained by means of techniques/methods which have conventionally been used in a number of applications and have a long safety record.

My opinion is this: Crispr/Cas9, whether used for genome editing, targeted mutagenesis, or even to make transgenics is genetic modification, but genetic modification can be just as safe as old mutagenesis methods. So what do we need instead of the current genetic modification directive?

First, one could include genome edited and targeted mutagenesis products among the exclusions to the directive. There is no reason to think they’d be any less safe than varieties developed by traditional mutagenesis or by crossing. In fact, the new techniques will give you fewer unexpected other variants as side effects. However, EU law does not seem to acknowledge that kind of argument. There would need to be a new law that isn’t based on the precautionary principle.

Second, one could reform the entire directive to something less draconian. It’s not obvious how to do that, though. On the one hand, the directive is based on perceived risks to human health and the environment of genetic modification itself that have little basis in fact. Maybe starting from the precautionary principle was a reasonable position when the directive was written, but now we know that transgenic organisms in themselves are not a threat to human health, and there is no reason to demand each product be individually evaluated to establish that. On the other hand, one can see the need for some risk assessment of transgenic systems. Say for instance that synthetic gene drives become a reality. We really would want to see some kind of environmental risk assessment before they were used outside of the lab.

Skype a scientist

Skype a scientist is a programme that connects classrooms to scientists for question and answer sessions. I have done it a few times now, and from the scientist’s perspective, it has a lot of reward for not that much work.

It works like this: the Skype a scientist team makes matches based on what kind of scientist the teacher asks for; the scientist writes a letter (or it could be a video or something else) about what they work on; the students prepare questions; and the scientist tries to answer.

One thing I like about the format is how it is driven by student questions, turning the conversation to things students actually want to know, and not just what the the scientist (me) believes there’s a need to ‘explain’ (scare quotes used to imply scepticism). Of course, the framing as a classroom exercise, the priming by the letter, and the fact that the questions pass through the teacher influence the content, but still. I also like how some students ask questions that I suspect are not entirely serious, but that still turn out to be interesting. Something I like less is how each session still is kind of a monologue with little interactivity.

I think it has gone reasonably well. I hope my answers will get more polished with time. Another thing I need to get better at is extracting useful feedback from the teachers to improve what I do. They’ve all said positive things (of course, how else could they respond?), but I’m sure there are all kinds of things I could improve.

Here, enjoy some of the questions I’ve gotten! I won’t answer them here; you will have to sign up your classroom for that. I have organised them into categories that I think reflect the most common types of questions.

Pig and chicken genetics

What are some mutations in pigs that you see?

Have you ever encountered a chicken that had something about it that surprised you?

What kinds of chickens live the longest?

What is significant about the DNA of pigs and chickens?

What is the most pervasive genetic disorders in pigs and chickens?

Which genes have the highest demand from industry?

Evolution

If certain traits are dominant and humans have been around for 6 million years, how do we not have all those dominant traits?

What came first, the chicken or the egg?

Does the DNA of chickens and pigs have any similarity to humans — if so, what percent is common?

When were pigs domesticated and what were they domesticated from?

Hard questions

Are science and religion compatible?

Can genetic engineering lead to the creation of a super-race?

Do you think that, if extra-terrestrial life was found, a breeding program between humans and aliens could exist to create hybrids?

Do you think you could genetically modify pigs to create the perfect bacon?

Can you genetically modify an organism to make it more clever?

Will we be able to genetically modify humans with features from other organisms such as gills, not just single gene traits?

What do you think is the next big genetically modified breakthrough on the horizon?

How far away are we from being able to clone a human (like Dolly)?

Have you researched genes designed to protect chickens or pigs from super bacteria resistant to antibiotics?

Personal stuff

Do you ever get to dissect anything?

What is the most exciting part of your job?

What is your favourite complex trait?

Have you always been interested in science?

What makes your job so important that you are willing to move countries?

Why did you choose to study genetics?

Do you prefer group or solo work?

Are you under intense pressure in your job?

What are you looking forward to working on in the future?

The practice of science

What materials do you use in your research?

Who decides what you research?

How do you use computers to research genes and DNA?

What kind of technology/equipment do you use?

Why do you research pigs and chickens?

På dna-dagen: dna-metaforer

Det finns olika metaforer för deoxyribonukleinsyran och vad den betyder för oss. Dna kan vara en ritning, ett recept, ett program eller skrift.

Det är nästan omöjligt att säga något om molekylärgenetik utan metaforer. Med kvantitativ genetik går det lite lättare, i all fall tills de statistiska modellerna och beräkningarna kommer fram. Kvantitativ genetik handlar om saker som alla kan se i vardagen, som familjelikhet och släktskap. Molekylärgenetik handlar om saker som, i och för sig finns i det allmäna medvetandet, men inte syns omkring oss.

Men metaforer kan vara ohjälpsamma och leda tanken fel. Bilden av dna som en ritning av organismen kan verka för enkel och leda tanken till genetisk determinism. Nu vet jag, trots att jag ska föreställa ingenjör, inte mycket om ritningar. På flera sätt är det inte så tokigt: en ritning representerar det som ska byggas med ett specialiserat bildspråk i en lägre dimension. Ett hus är i 3D, men en ritning i 2D. Proteiner är tredimensionella; den genetiska koden beskriver dem i en dimension. Men det kanske är sant att ordet ”ritning” (eller ”blåkopia”) för tanken till något som är för exakt och för avbildande.

Ett alternativ är att dna är ett recept (det är många som föreslagit det; bland annat Richard Dawkins i The Blind Watchmaker, 1986). Receptet har den fördelen att det beskriver en process med både ingredienser och instruktioner. Det är lite som organismens utveckling från ett befruktat ägg till en vuxen. ”Tillsätt maternell bicoid i ena änden och nanos i andra änden; låt proteinerna blandas fritt”, och så vidare (Gilbert 2000). En annan fördel är att det naturligt påminner om att dna inte är allt. Samma recept med lokala skillnader i ingredienser och improvisationer från den som lagar blir olika anrättningar. Å andra sidan överdriver receptet vad som finns i dna. Vilka gener som uttrycks var och när är ett samspel av dna och de proteiner och rna som redan finns i en cell vid en viss tidpunkt.

Eller så är dna ett program. Program är också instruktioner, så det har samma fördelar och nackdelar som receptet på den punkten. Å andra sidan är program abstrakta och fria från konkreta ingredienser och associationer till matlagning. Lite som en ritning låter det mekaniskt och exakt. Det spelar tydligt också roll vad dna skulle vara en ritning av eller ett recept på. Det är viss skillnad att kalla dna en ritning av proteiner än ett recept på en organism.

Till sist finns det metaforer inskrivna i själva terminologin. När genetiker pratar om dna, hur det förs vidare och används, pratar vi om det som ett skriftspråk. Det kallas kopiering när dna reproduceras när celler ska dela sig. Det kallas transkription, alltså kopiering men med en ton av överföring till en annan form eller ett annat medium, när rna produceras från dna. Det kallas translation, översättning, när rna i sin tur fungerar som mall för proteinsyntes. Till råga på allt skriver vi dna med ett alfabet på fyra bokstäver: A, C, T, G. Det är en bild som är så passande att den nästan är sann.

(Den 25 april 1953 publicerades artiklarna som presenterade dna-molekylens struktur. Därav dna-dagen. Gamla dna-dagsposter: Genetik utan dna (2016), Gener, orsak och verkan (2015), På dna-dagen (2014))

NASA and Orphan Black

A few months ago I wrote a post about the (fictitious, and also evil) clone experiment in Orphan Black. I said that comparison of complex traits between a handful of individuals isn’t, even in principle, a ”scientifically beautiful setup to learn myriad things”, but garbage. You can’t take two humans, even if they’re clones, put them in different environments, and expect to learn much of anything.

Funnily enough, it seems like NASA has been doing just that with the NASA twin study: there are two astronauts who are twins, and researchers have compared various things between them and before/after one of them went to space. Of course, those various things include headline-attracting assays like telomere length and DNA methylation (including ”epigenetic age” — something like Horvath 2013, I assume).

The news coverage has been confused — mixing up DNA methylation, gene expression and mutation. But can one blame news outlet for reporting about ”7% changes to his DNA” and ”space genes” when the press release said this:

Another interesting finding concerned what some call the “space gene”, which was alluded to in 2017. Researchers now know that 93% of Scott’s genes returned to normal after landing. However, the remaining 7% point to possible longer term changes in genes related to his immune system, DNA repair, bone formation networks, hypoxia, and hypercapnia.

Someone who knows some biology can guess that this doesn’t refer to mutation, but it’s not making things easy for the reader, and when put like that, the 7% could be DNA methylation, gene expression, or something else transient and genomic. (They’ve since clarified that it was gene expression — in some sample; my bet is on white blood cells.)

Now that we’ve made fun of NASA a little, there are some circumstances when we can learn useful things from studies of even a single individual. For example, if Chaser the Border Collie can learn the names of 1000 toys, and learn new toy names through reasoning by exclusion (Pilley & Reid 2011), then we can safely assume that this is within the realm of dog abilities. Another example is a reference genome, which in the best case is made from a single individual, ideally an individual who is as homozygous as possible. When comparing the reference genome to that of other species, we feel confident enough to publish genome papers with comparisons of gene content, gene family evolution, and selection on protein coding sequences over evolutionary timescales. But when it comes to functional genomics, many variable molecular trait measurements all along the genome? No.

The study is not out. It may be better than the advertisement. It’s seems they’ve compared the two men before and after, so they can get some handle on differences that came about in the years leading up to the study. And maybe they’ve run a crazy number of technical replicates to make sure that the value they get from each data point is as a good measurement as possible. And maybe there is data on what happens with these kinds of assays when people do other strenuous things, putting the differences into context. Maybe.

Literature

Pilley, John W., and Alliston K. Reid. ”Border collie comprehends object names as verbal referents.” Behavioural processes 86.2 (2011): 184-195.

Horvath, Steve. ”DNA methylation age of human tissues and cell types.” Genome biology 14.10 (2013): 3156.

Selected, causal, and relevant

What is ”function”? In discussions about junk DNA people often make the distinction between ”selected effects” and ”causal roles”. Doolittle & Brunet (2017) put it like this:

By the first (selected effect, or SE), the function(s) of trait T is that (those) of its effects E that was (were) selected for in previous generations. They explain why T is there. … [A]ny claim for an SE trait has an etiological justification, invoking a history of selection for its current effect.

/…/

ENCODE assumed that measurable effects of various kinds—being transcribed, having putative transcription factor binding sites, exhibiting (as chromatin) DNase hypersensitivity or histone modifications, being methylated or interacting three-dimensionally with other sites — are functions prima facie, thus embracing the second sort of definition of function, which philosophers call causal role …

In other words, their argument goes: a DNA sequence can be without a selected effect while it has, potentially several, causal roles. Therefore, junk DNA isn’t dead.

Two things about these ideas:

First, if we want to know the fraction of the genome that is functional, we’d like to talk about positions in some reference genome, but the selected effect definition really only works for alleles. Positions aren’t adaptive, but alleles can be. They use the word ”trait”, but we can think of an allele as a trait (with really simple genetics — its genetic basis its presence or absence in the genome).

Also, unfortunately for us, selection doesn’t act on alleles in isolation; there is linked selection, where alleles can be affected by selection without causally contributing anything to the adaptive trait. In fact, they may counteract the adaptive trait. It stands to reason that linked variants are not functional in the selected effect sense, but they complicate analysis of recent adaptation.

The authors note that there is a problem with alleles that have not seen positive selection, but only purifying selection (that could happen in constructive neutral evolution, which is when something becomes indispensable through a series of neutral or deleterious substitutions). Imagine a sequence where most mutations are neutral, but deleterious mutations can happen rarely. A realistic example could be the causal mutation for Freidreich’s ataxia: microsatellite repeats in an intron that occasionally expand enough to prevent transcription (Bidichandani et al. 1998, Ohshima et al. 1998; I recently read about it in Nessa Carey’s ”Junk DNA”). In such cases, selection does not preserve any function of the microsatellite. That a thing can break in a dangerous way is not enough to know that it was useful when whole.

Second, these distinctions may be relevant to the junk DNA debate, but for any research into the genetic basis of traits currently or in the future, such as medical genetics or breeding, neither of these perspectives is what we need. The question is not what parts of the genome come from adaptive alleles, nor what parts of the genome have causal roles. The question is what parts of the genome have causal roles that are relevant to the traits we care about.

The same example is relevant. It seems like the Friedriech’s ataxia-associated microsatellite does not fulfill the selected effect criterion. It does, however, have a causal role, and a causal role relevant to human disease, at that.

I do not dare to guess whether the set of sequences with causal roles relevant to human health is bigger or smaller than the set of sequences with selected effects. But they are not identical. And I will dare to guess that the relevant set, like the selected effect set, is a small fraction of the genome.

Literature

Doolittle, W. Ford, and Tyler DP Brunet. ”On causal roles and selected effects: our genome is mostly junk.” BMC biology 15.1 (2017): 116.

Nessa Carey ”Junk DNA”

I read two popular science books over Christmas. The other one was in Swedish, so I’ll do that in Swedish.

Nessa Carey’s ”Junk DNA: A Journey Through the Dark Matter of the Genome” is about noncoding DNA in the human genome. ”Coding” in this context means that it serves as template for proteins. ”Noncoding” is all the rest of the genome, 98% or so.

The book is full of fun molecular genetics: X-inactivation, rather in-depth discussion of telomeres and centromeres, the mechanism of noncoding microsatellite disease mutations, splicing — some of which isn’t often discussed at such length and clarity. It gives the reader a good look at how messy genomics can be. It has wonderful metaphors — two baseball bats with magnetic paint and velcro, for example. It even has an amusing account of the ENCODE debate. I wonder if it’s true that evolutionary biologists are more emotional than other biologists?

But it really suffers from the framing as a story about how noncoding DNA used to be dismissed as pointless, and now, surprisingly, turns out to have regulatory functions. This makes me a bit hesitant to recommend the book; you may come away from reading it with a lot of neat details, but misled about the big picture. In particular, you may believe a false history of all this was thought to be junk; look how wrong they were in the 70s, and the very dubious view that most of the human genome is important for our health.

On the first page of the book, junk DNA is defined like this:

Anything that doesn’t code for protein will be described as junk, as it originally was in the old days (second half of the twentieth century). Purists will scream, and that’s OK.

We should scream, or at least shake our heads, because this definition leads, for example, to describing ribosomes and transfer-RNA as ”junk” (chapter 11), even if both of them have been known to be noncoding and functional since at least the 60s. I guess the term ”junk” sticks, and that is why the book uses it, and why biologists love to argue about it. You couldn’t call the book something unspeakably dry like ”Noncoding DNA”.

So, this is a fun a popular science book about genomics. Read it, but keep in mind that if you want to define ”junk DNA” for any other purpose than to immediately shoot it down, it should be something like this:

For most of the 50 years since Ohno’s article, many of us accepted that most of our genome is ”junk”, by which we would loosely have meant DNA that is neither protein-coding nor involved in regulating the expression of DNA that is. (Doolittle & Brunet 2017)

The point of the term is not to dismiss everything that is not coding for a protein. The point is that the bulk of DNA in the genome is neither protein coding nor regulatory. This is part of why molecular genetics is so tricky: it is hard to find the important parts among all the rest. Researchers have become much better at sifting through the noncoding parts of the genome to find the sequences that are interesting and useful. Think of lots of tricky puzzles being solved, rather than of a paradigm being overthrown by revolution.

Literature

Carey, Nessa. (2015) Junk DNA: A Journey Through the Dark Matter of the Genome. Icon Books, London.

Doolittle, W. Ford, and Tyler DP Brunet. (2017) ”On causal roles and selected effects: our genome is mostly junk.” BMC Biology.