genetic – Sciblogs Sciblogs Wed, 22 Nov 2017 23:54:06 +0000 en-US hourly 1 genetic – Sciblogs 32 32 Put the brakes on ‘gene drives’ for predator control, say researchers Thu, 16 Nov 2017 21:14:02 +0000 New Zealand wants to get rid of predators. But some of the genetic tools under consideration for the task could have disastrous consequences if they spread beyond our shores, warn researchers.

Last year New Zealand boldly announced its ambitious Predator Free 2050 goal, and just yesterday unveiled a detailed strategy for reaching the goal. Investigating the potential of new technologies, such as gene drives, forms a key part of the strategy.

Today researchers from the US and New Zealand have issued a stern warning, urging that any use of such technologies must have built-in safeguards. In an article published today in PLOS Biology, Professor Neil Gemmell from Otago University and Assistant Professor Kevin Esvelt of MIT highlight the possible consequences of the accidental spread of existing ‘self-propagating’ gene drive systems.

What’s a ‘gene drive’?

Gene drive systems distort the rule that there is a 50:50 chance of a gene copy being passed on. This promotes the inheritance of a particular copy of a gene from the parent to offspring. When coupled to a genetic trait that affects an individual’s survival or ability to reproduce, it becomes a powerful tool that can be used for population control or even local elimination.

Credit: Kevin Esvelt

‘A mistake’

Back in 2014, Prof Esvelt authored one of the first articles outlining how self-propagating gene editing technology could be used for conservation purposes.

Today, he retracts that suggestion:

We now believe that inclusion was a mistake: such drive systems lack control mechanisms and are consequently highly invasive.

While Profs Gemmell and Esvelt support the idea of the Predator Free 2050 initiative, they say that the release of a gene drive system carries the risk that some of the target species may hitch a ride to other countries and start spreading the gene drive system there.

“The bottom line is that making a standard, self-propagating CRISPR-based gene-drive system is likely equivalent to creating a new, highly invasive species – both will likely spread to any ecosystem in which they are viable, possibly causing ecological change.”

“We are highly skeptical that it would be safe to release a self-propagating drive system capable of spreading beyond the target local population unless international spread is the explicit goal. Even building such a construct in laboratory containment within a region harboring the target species poses the risk that an accidental escape might eventually affect everyone who shares an ecosystem with that species. For rats and mice, that constitutes most people on Earth. While these species are pests in many contexts, they also underpin important ecosystem services in large areas of the globe.

They also warn that such an escape would shatter trust in the use of the technology for other purposes, such as controlling mosquito populations to prevent the spread of malaria.

“CRISPR-based gene drive is arguably the technology most likely to help eradicate human scourges such as malaria and schistosomiasis. It would be a profound tragedy if New Zealanders—or anyone else—inadvertently caused an international incident and consequent loss of public confidence in scientists and governance that interfered with its use. Going by past examples of accidents and misconduct in diverse fields of science, and particularly the effects of tragic outcomes in gene therapy trials, any unauthorized release of a gene drive system would quite likely delay applications by a decade or more. For malaria alone, the cost of that delay could be measured in millions of otherwise preventable deaths.”


Aedes aegypti mosquito
A loss of trust in genetic technologies could undermine efforts to control populations of malaria-spreading mosquitoes. Image source: CDC.

Read more about the research on

Exploring alternatives

When it comes to genetic technologies, self-propagating gene drives aren’t the only game in town. The authors of the new article outline alternatives including Professor Gemmell’s “Trojan female” technique, Professor Esvelt’s recent “daisy drive” technology and “precision drive.” These approaches that target mutations known to be unique to a particular population are safe enough to consider, they write.

Reaction from New Zealand researchers

The Science Media Centre has collected extensive commentary from New Zealand researchers. Amongst the commentary collected there was overwhelming agreement that any work on gene editing technologies must proceed with extreme caution.  Here’s just a sample of the responses.

Dr Andrea Byrom, Director  of New Zealand’s Biological Heritage National Science Challenge, highlighted that any use of genetic technologies was still years away:

Contrary to the hype, gene drive technology for mammals is still highly theoretical, and I must emphasise that no such research is currently being conducted in New Zealand. We have literally years of technological development ahead of us before we could proceed with deployment in the field, and future use of gene editing technologies, including gene drive, will be in the hands of the public of New Zealand to decide.”

Prof Barry Scott from the Institute of Fundamental Genetics at Massey University said:

Given the scale of the pest issue in New Zealand and the urgency with which we need to find better solutions to prevent further extinctions there is a great temptation to look for ‘silver bullets’.

Genetic solutions are a promising new tool but we do need to proceed with caution and a sound understanding of the biology underpinning the control measures. It is crucial that we continue to invest in research in these areas, especially those directly relevant to New Zealand. There is also a need to put in place a framework for community trust building so that societal values and ethics are taken into account as the science develops.

Dr James Russell, conservation biologist, University of Auckland, also endorsed a cautious approach but pointed out that much of the focus so far has been on gene drives which affect fertility in the target species:

There are other gene edits one could make, especially those that pair the target species with its recipient ecosystem, e.g. imagine trivially giving all rats in New Zealand a peanut butter allergy and then we feed them all peanut butter. Matching the genetic mode of action to an environmental stimuli might be powerful indeed.

A less-discussed aspect of the issue, cultural  accountability, was highlighted by Melanie Mark-Shadbolt, Māori Manager for New Zealand’s Biological Heritage National Science Challenge:

From an indigenous researchers perspective what this paper does do is clearly highlight two growing concerns in the research space.

The first being an increasing lack of cultural accountability in academic journals who seem happy to publish anything without thought, consideration, or commentary from the communities those papers have extracted from, taken swipe at, or made promises to. While we expect individual researchers to be responsible and accountable for their work (and in fact Prof Esvelt calls for this) academic journals seem to be immune to such requirements.

The second issue is what I deem bad research-dating behaviour, or rather how to build respectful relationships with indigenous peoples/communities. Increasingly researchers are seeking opportunities to work with and engage with indigenous communities i.e. Māori. Relatively few, however, are actually committed to investing their time into building long-term relationships, despite being continually told that that is what is required.

Read more on the Science Media Centre website.

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Autism is mostly genetic again Tue, 24 Oct 2017 01:04:49 +0000 Ever since Rain Man, autism has been a condition du-jour for those touting (fake) ’wellness’ remedies, opposing vaccines, and general head-nodding concern. Some claim autism is caused by any number of things, offering just many remedies offered to “treat” it. Recent research reminds us that autism is mostly genetic.

People with autism, or autism spectrum disorder, have difficulty in social communication and interaction. One autistic computer programmer wrote to me that he preferred to interact by email, rather than meet with me in person. It can also feature repetitive behaviours such as stacking the cans in the feature image for this article, ordering toys in rows, and strong interests on particular narrow topics.

Hollywood movies like Rain Man and TV dramas are more inclined to idolise ‘autistic savants’. Curiously Kim Peek, the real-life inspiration for the Rain Man character played by Dustin Hoffman, was not autistic. Brain scans showed that he had corpus callosum agenesis as described towards the end of my earlier article, The mutant PRICKLE and the split brain.

For a more real-to-life setting, a film outlining features of autism in young kids can be found at the ASDinfoWales website. One excellent summary of autism myths and facts, with research references, can be found at the UK Austistic Society’s Autism facts and history page.

Placing toys in ordered rows can be important for some autistic kids. (Source: Wikipedia, GNU Free Documentation License. Edited to preserve anonymity of the subject owing to model license concern.)

There is a long history of autism being considered mostly genetic; autism is often said to be the “most genetic” of the neurodevelopmental disorders. For example, twin studies point at high rates of heritability, around 90%. Similarly, siblings are 15-30 times more likely to have autism than the general population.

It’s also increasingly thought to start very early, before the chid is born. Autism is more frequently found in boys, and there are associations with parental age and other factors.

If you were to peek into the research publications estimating the extent to which autism is inherited or genetically-determined—two slightly different things!—you’d find a thicket of numbers and arguments, with values from around 60% to 90%, with a few outliers.

It’s such a jungle, you’d want to go in armed with a machete in each hand to cut your way through the mess. (And toss on a bandolier or two, and a bunch of automatic weapons, Indiana Jones style just to look the part.)

One study latched on by some of those touting “remedies” for autism is a study suggesting a hereditariness of about 50%. Researchers made some suggestions why this study offered a much lower estimate of hereditary contribution to autism than other estimates. A fresh re-examination of the dataset comparing different methods shows the variation in autism cases is mostly genetic, at around 83%.

These statistics are often incorrectly reported as saying something about each autistic person. It actually tells us about what fraction of the variation in autistic people as a large group is due to inheritance. There’s also one type of genetic contribution that is not inherited that is not considered in hereditary estimates: “brand new” (de novo) mutations.

The researchers used same dataset they previously used—over 2 million Swedish children—this time applying a method “used by previous studies in the field”, finding the heritability to be 83%, rather than the 50% they previously found.

Clearly the method used to estimate heritability matters. In their earlier work, they used a mathematical model that included “time to ascertainment”: when it was that the child was diagnosed. One concern was that it might the hereditariness to be underestimated. (Siblings are often diagnosed at quite different times, and sometimes under diagnosed.) The re-examination of the data suggests this is what has happened.

Re-examination of assumptions of previous work is part of how science proceeds. It must seem a slow, one step back and a step or two forwards process to the public, but that’s how it goes.

It also conflicts with the tidy stories media want to tell. If you were to go out and read articles about this recent estimate, you’d find very little pointing to the wider, messier story I alluded to earlier.

These estimates are quite complex. They also rely on a bunch of assumptions. I suspect that it will be difficult, possibly not even practical, to try obtain a “correct” figure beyond the broad observation that autism is strongly genetic.

Beyond diagnostic and sampling issues, the genetics of autism itself provides challenges. There are small number of “simple” (Mendelian) genetic mutations that might explain perhaps 10% or so of autism cases. For these few cases, an association between autism and a well-defined mutation that is inherited in a simple way has been found. There is also evidence that a very large number of genes is involved, each contributing to a small fraction of the cases.

Furthermore, there is the issue of mutations that have arisen anew in the child. (I’ve previously written on one study of these in, Autism genetics, how do you copy?) Each of us has perhaps a hundred or so mutations not present in either of our parents. Most of these mutations do nothing, and have no effect on us, but some types of these so-called ‘de novo’ mutations are associated with different conditions.

There tend to be more of these de novo mutations in children of older parents, and having older parents has been associated with autism. For example, sperm get slightly more mutations in them as the father ages. As they’re not inherited from the parents, these de novo mutations don’t add to the “hereditary” side of the tally. They’re considered to be “environmental” even though they’re also clearly a genetic thing! (The trick is to notice the difference between ‘inherited’ and ‘genetic’: they’re genetic, but not inherited.)

The complexity gets worse as you look further!

One thing that might be useful is more information on physical things we can record and observe in genome data. That would require very large collections of genome data, accompanied by good medical records. There are some attempts to look at aspects of this. They each look at one type of genetic change, in subsets of the genome data. Essentially they’re taking educated guesses at what might be useful to look at. It’s a reflection of the technology and numbers involved. Simply surveying the genomes outright, as whole genomes, will involve even more genomes than the current large-scale genome sequencing efforts are producing. (And a lot of money!) As one example GenomicsEngland report they have sequenced just over human 36,000 genomes as I write. Compare that to the two million-plus children used in the recent estimate of hereditariness.

It might, then, be a case of waiting for the technology and costs to become suitable — which they will, and surprisingly soon: years, rather than decades.

Other articles on Code for life

The mutant PRICKLE and the split brain

Tracking disease and human migration through genetics

Preserving endangered species – of gut microbes

Autistic children and blood mercury levels

Are too many vaccines too soon harmful?

Visual illusions, change blindness and autism

Autism genetics, how do you copy?


JAMA. 2017 Sep 26;318(12):1182-1184.

The Heritability of Autism Spectrum Disorder.


PMID: 28973605 DOI: 10.1001/jama.2017.12141


My thanks to a colleague for supplying me with a copy of the paper.

The free personal registration for JAMA is limited those in the USA. I’ve no idea if this would let me get a full copy of the research paper if I faked being from the USA with VPN!

Featured image

Source: Wikipedia, used under GNU Free Documentation License. “Quinn, an ~18 month old boy with autism, obsessively stacking cans. Date: Late 2002. Place: Walnut Creek, California. Photographer: Andwhatsnext. Scanned photograph. Credit: Copyright (c) 2003 by Nancy J Price (aka Mom)”

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Triple S rated- sex, salmon and scicomm Fri, 06 Mar 2015 12:10:48 +0000 Milking male salmon- it's all in the hand hold.
Milking male salmon- it’s all in the hand hold.

A long time ago in a place not so far away, a young research scientist spent several weeks each colour-changing autumn ejaculating male salmon for their rich, milky sperm. It certainly wasn’t your everyday job and it wasn’t all as glamorous as it perhaps sounds. In fact it was about as removed from the ivory tower fantasy of academia as possible. And that young scientist was me.

We stood for hours and hours in cold raceway water at the hatchery, with reeking fish-slime infused polypropylene gloves, rubber jacket and lots of layers to keep warm. Forcing oneself to eat sandwiches at lunch with fingers that smelled like salmon. Sitting in an office with the Hatchery lads, entering their male bastion unflinchingly and being eventually accepted I think as they witnessed the hard work we put in and our lack of hierarchy of scientist infiltrators versus hatchery staff. We were all one.

A typical male salmon with its gonads for scale.
A typical male salmon with its gonads for scale.

And the day didn’t end once the males were all spent or used. We might have then to spend some more hours setting up fertilisations with female eggs and some of our milt at the raceway, mixing measured eggs and milt precisely and quickly before putting into tall jars with flowing water.

Then the day went longer still-into the small hours of the morning analysing their sperm on a microscope in the chilled down aquarium back at university. And up again early to do it all again. For weeks.

All of this with two other incredible comrades, the Salmon Sisters we called ourselves- a PhD student and a technician and me.

Having no prior milt stripping experience it was a case of learning rapidly on the job. Field seasons were short and the scale of the study large. Lots of males swimming lazily waiting in a raceway to be netted, gently pulled out of the water, and scanned to identify PIT tags, the unique numerical name they held for each fish.

Getting jars ready for fertilisation experiments
Getting jars ready for fertilisation experiments

Then the salmon hugged close to my stomach. Working out just where to start gently squeezing with thumb and fingers wrapped around their abdomen and then maintain that pressure running from head-end to tail-end was a skill that took time but I got pretty expert at it.

If I did it just right and the male was ripe and ready the white jet of milt flowed forcefully; one of the other Sisters carefully catching it with a plastic pottle until ejaculation ceased. The other Sister sat recording data on a computer at a table next to us. Then when finished, the male got put gently back into the water on the other side of the fence in the raceway.

We called this the “cigarette moment”- the male lying immobile for 30 seconds or so before coming to with a flick of his tail and swimming off- either disgusted or in bliss, who would know?

A precocious male gets milked.
A precocious male gets milked.

The little precocious males were my favourite. So tiny because they mature a whole year earlier and put most of their energy into reproduction, making them squishy testes-filled cuddliness. And they could sure produce a lot of milt when squeezed by my hands. Their strategy is not to win the female but to sneak in when fertilisation is taking place and squirt their milt in adding to the parentage. In the wild, each lot of salmon embryos may have several fathers- alpha male, a beta male or two who also shoot in and shoot their load and precocious or sneaker males.

Unlike humans, fish sperm doesn’t tend to be viable for days. Once that milt hits water, it’s activated and then it only is motile and  swimming madly for 1 minute or so before it runs out of internal ‘steam’. So reproduction for them is a rapid fire  pressure filled act. Chinook salmon have just one breeding season. They might mate (or sneak into a mating act) many times over several weeks but then it’s game over for them.

Unless landlocked, they’re been maturing out at sea, orange fleshed with beta-carotene from the food they have consumed. When it’s their year to mate (usually age 3 or so in New Zealand) they re-find their stream or river of origin and head back up it. Heading from saltwater to freshwater triggers large scale physiological changes. Their digestive system starts to break down and they stop eating.

Most of their remaining energy is then diverted to pumping up those testes. Over the season then, the fish without energy coming in, literally start to decay. Their skin starts rotting and falling off. Handling them to strip them in the last couple of weeks was unpleasant. I do not really eat salmon to this day as a result.

End of season male salmon.
End of season male salmon.

Learning all of this was enthralling. The aim of the research was too- trying to use salmon as a model to better understand the impact that mutations in a special type of DNA (mitochondrial DNA) that organisms have within their cells have on male infertility. This DNA is in a separate location to our chromosomal DNA within something called the mitochondria of every cell.

There could be consequences on the viability of populations, especially endangered ones, of these mutations. This is due to mitochondrial DNA being passed down only from mothers, which means if sperm are affected by a mutation it won’t be selected against and mothers may give the mutant DNA to their sons.

It was just too much exciting information not to share. So I did. I spent some of my weekend nights heading out with my friends to Christchurch bars, where when a guy asked me what I did, I replied “I wank salmon”. Talk about a conversation starter.

If they could get over their obvious shock and take the bait it lead to some hilarious conversations about just what exactly I did and even demonstrations of how to milk a salmon. This was I realise now science communication in a casual setting. I got an awful lot of people excited about salmon sperm and science back then. And my friends still remember those nights with much hilarity and will do so for decades to come.

Science communication takes many forms and next week in the first every #SciCommNZ chat (Wed 11th March 2030-2130 NZT) we will be exploring just that. Such a casual form of scicomm isn’t going to get recognition at present and it’s certainly not going to lead to any awards. However, I think despite being underrated this form of science communication is actually highly important.

Perhaps we should be paying more attention to and training scientists and science communicators for more casual opportunities. Perhaps we should be getting out of our comfort zones and challenging ourselves as I did. Perhaps we should be more controversial and less constrained or restrained.

All of my salmon, sex and scicomm experiences came back to me a few days ago when the wonderful scientist and science communication @Dr_Mel_Thomson started a Twitter conversation that seemed a fitting occasion to dust off the salmon ejaculation stories. That conversation had many of us rolling around the floor in laughter across the world. This tweet in particular elicited a particularly hilarious response.




Let’s value all the forms of science communication out there. Let’s look at how humans interact naturally and tap into that to improve our science communication efforts. A bar may be just the very place to foster science literacy (and not necessarily in a Cafe Scientifique kind of way). And if you can get sex into the science conversation, well that helps too, because sex always sells.

If you want to see the Twitter conversation that spawned (pun intended) this blog post you can find it here.

The conversation lead to a small list of scientists who are engaging in stand-up comedy. They include:

Brian Malow @sciencecomedian

Sean M Elliott @SeanMElliott

Ben McKenzie @labcoatman

Tom Lang @Langaround

Pam Rana

Simon Pampena @mathemaniac

Dara O Briain @daraobriain

Strikes me that there is a shortage of women on this list. Maybe there’s a place for Mel and I after all.

* This post is dedicated to the other two sensational Salmon Sisters, Patrice Rosengrave and Kath McBride, with whom I could not have done this project. Kath very sadly passed away recently. 

The salmon sisters

** The work conducted during this project was supported by the Marsden Fund and my postdoctoral mentor was the effervescent Professor Neil Gemmell who let us all become salmon enthusiasts.

Salmon 2

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