A cleaner crisp(e)r way of editing the code!

We hear so much about CRISPR (discussed in a previous blog) and gene editing these days that it feels like the technique has been around for a decade (or more), and not something relatively unheard of before 2012.  Yet it's still an advance very much in its infancy, and one not without a healthy (no pun intended!) burden of controversy weighing it down. 

The heaviness surrounding the use of the CRISPR-Cas9 system lies in its potential not only to edit and correct disease-causing mutations or defective genes such that we revert to a normal genotype and phenotype, but also due to the fact that the technique may very well be open to "abuse" (or perhaps misuse) by those wishing to alter some part of their non-diseased phenotype. We want our baby to have blonde hair and blue eyes, for example. 

In a striking new development set to make the CRISPR technique an even more disruptive technology, one of the pioneers in the field just published a paper in Cell, yesterday, outlining the discovery of a new nuclease, Cpf1. Feng Zhang of the Broad Institute in Cambridge (MA) felt that as exciting and useful as the CRISPR-Cas9 system is, there was still benefit in seeking to refine it, and refine it he just did.

As technically brilliant as CRISPR editing is, there are a few drawbacks which clearly niggled at Zhang, who returned to the world of bacteria and went hunting for alternates to Cas9.  Having discovered Cpf1 in bacteria, his team isolated Cpf1 from some sixteen different bacterial strains and found two that could cut human DNA.Zhang then went about more fully characterising its properties in comparison to Cas9. 

One reason why Cas9 is not a perfect choice lies in the fact that it needs two guide RNAs to facilitate appropriate cutting of DNA; Cpf1 needs just one. Additionally, Cas9 is a considerably larger protein than Cpf1; coupled to the need for just one guide RNA, this makes Cpf1 easier to package and deliver to cells. Furthermore, and by no means least, Zhang discovered that both the sites of cleavage and their nature were distinct between the two nucleeases; this difference potentially makes the cutting and insertion of DNA by Cpf1 a much more accurate and efficient process - an explosive finding. 

Cas9 cuts both strands of DNA at the same position, leaving the DNA with blunt ends, the repair of which is hard to control and prone to errors. Cpf1 on the other hand leaves sticky end overhangs, which should make it much easier to control the appropriate insertion of the appropriate piece of exogenous DNA into a gene. As explained bu Zhang - "The sticky ends carry information that can direct the insertion of the DNA. It makes the insertion much more controllable" - which can only be a good thing. 

There's an unexpected bonus in all of this, which centres on the ongoing and brutal legal dispute over who-discovered-what in the CRISPR-Cas9 story. The two contenders in this dispute are the Broad Institute of MIT-Harvard (including Zhang et al.) and UC Berkeley, whose Jennifer Doudna is a major player along with her collaborator Emmanuelle Charpentier. In what may be true irony, even though Zhang and the Broad hold 10 patents on the technology, it is Doudna in particular who is often singled out by the media as the discoverer of CRISPR-Cas9. So one of the two sides is clearly winning the patent war and the other is winning most of the credit for the discovery. 

It may all come down to that staple of laboratory life - the lab notebook - given that the Regents of the University of California have asked the USPTO to approve "patent interference" to determine who was the inventor in those 10 patents belonging to Zhang and the Broad. It's going to get messy, almost certainly, and even the commercial end of this story is already messy, with both Zhang and Doudna originally listed as co-founders of Editas Medicine, a Cambridge-based biotech company set up to develop medicines based on the CRISPR system. Doudna has since exited, but not before selling her patent rights to another biotech, the UK's CRISPR Therapeutics, the founder of which is none other than, wait for it, a certain Emmanuelle Charpentier! 

There's gold in them hills, with Editas having raised additional funds totalling $120M in August, and a new player on the scene, Intellia, having raised some $70M in recent weeks. No shocker that Intellia is connected to Berkeley, by the way. But there's a lot more than mere millions at stake here, not least because scientists often care way more about credit, than their line of creidt! Some talking heads are already earmarking Doudna and Charpentier for the Nobel Prize, and you can bet that this rankles Zhang and MIT. 

It's fascinating stuff of course, and full of the passionate competitiveness and resulting drama that is at the heart of groundbreaking scientific discovery. With the recent patent interference request by the Regents of UC, it looks like it may well be a case whose outcome will come with its very own theme tune - "The Winner Takes It All" - because the USPTO is likely to come out squarely on one side or the other. This may just turn out to the scientific equivalent of the OJ Simpson trial and verdict, and you can expect some heavy duty (but non-violent!) fall-out if a severe injustice appears to have been done. 

Well, it's a simply gorgeous late September Saturday afternoon here in Montreal, and so I am off to get a few kilograms of baby back ribs onto the barbecue, smoking, as my trademarked "Belfast Cowboy Fiery Maple Hickory Smoke" sauce bubbles gently on the side. I've got some seriously hungry ranchers coming in later, so I better get to it. That's it for this one, so, until next time! :)

Unraveling the branches on the Tree of Life!

It took us roughly 3.5 billion years and minimally (but probably way more) some 2.3 million species, to get us to where we are today at the top of the tree of life, and now scientists have published the first draft of an open source "Tree of Life".  This public resource is intended to be a sort of "Wikipedia" for scientists and the public alike, exploring and explaining evolutionary relationships that essentially interrelate all lifeforms on the planet. 

This digital resource is available at Tree of Life and the idea is that people will add to it as new information becomes available and proven, although having said that, the site appears to be down currently, apparently due to all of the traffic it has seen since the release of the draft! But it's quite interesting that the creators of the Tree of Life (i.e. the digital version, not the living one!) have not only released the big picture, but also the data from which it was constructed as well as the source code. 

This tree was assembled via a collaboration involving eleven institutions but was not built from scratch; previous smaller trees including some with over 100,000 species in their branches were used to piece it all together. Roughly 500 of these smaller trees were used to build the bigger picture outlining how microbes, fungi, plants, animals and humans evolved and diverged from each other - and essentially underlining how brilliant Charles Darwin actually was in more recent human history. 

The BBC released a hugely popular documentary "Charles Darwin and the Tree of Life" which was narrated by the indefatigably passionate Sir David Attenborough, to celebrate the 200th anniversary of Darwin's birth and given the hundreds of thousands of views on YouTube alone, I felt it would be appropriate to share it on this blog regarding the Tree of Life. 

As brilliant as the creation of life on this planet unquestionably was and is, for us scientists it is interminably fascinating how all of these 2 million + species originated and evolved together and/or sequentially, which by a combination of some good luck and the precise swathe of the great evolutionary scythe ultimately led to the appearance of the humanoid lifeform currently dominating the planet. 

Had we not evolved as we did, and mankind's precursors had not escaped their roots and gotten "out of Africa", what would the world look like today? It's a mind-boggling question and as much as we (perhaps naturally) tend to assume that our appearance out of the jungle's "primeval soup" was inevitable, well, it;s hardly the case. As my mother asked me recently - "Well, if we evolved from apes, then how come they stopped evolving? Where are all the hominids today?"

There is a definitive line of thought that the unending need for water to feed the tree of life drove our ancestors towards the coastal waters in Africa, and it was the dietary changes there that fed the development of the Homo erectus brain. It is suspected that seafood and shellfish rich in fatty acids such as docosahexaenoic acid and arachidonic acid, facilitated the evolution of relatively small-brained hominids into those with increased brain size. The key requirement of these types of fatty acids for mammalian neuronal development may explain the very productive "accident" that the Homo species walked into when splashing around coastal rivers and lakes. 

This is by no means a proven theory, and for many the appearance of tools, and fire, and the cooking of meat is regarded as the key step in evolution that led to increased cranial size in hominids. But it seems that evidence of the regular and organised use of fire is not abundant pre-1 million years ago, when cranial size in hominids had measurably increased. It seems entirely possible that aquatic diets may have fed the developing brain, and the subsequent use of fire and cooked meat truly pushed us further along with the critical combination of increased brain size coupled to serious cognitive advances and blossoming intelligence. 

In any case, we got to where we are today, one way or another, and this first draft Tree of Life is an inspiring effort to explain it all. But it is a first draft, and it will be just as interesting to see how that tree evolves over time, being elaborated on with our increasing understanding of life on this planet. This tree will be used in the meantime to further scientists' efforts in drug discovery, improve agricultural yields in terms of both animals and plants, and to better understand and tackle infectious diseases. 

Now, speaking of dietary elements and brain power, I think it is time for this boy to get his hands on some Madagascar Morning Mellow thereby partaking of some solid caffeine to kickstart the day. Oh, and that coffee also came "out of Africa"! 

Prying the lid off and peering into PubPeer!

          

Earlier in the year, I brought up the irreproducibility issue that is apparently rampant in modern biological research, and how it had led to the creation of an anonymous forum where (usually) disgruntled individuals can vent and essentially critique published work online - we are of course talking about PubPeer - well, now the story evolves further with one of the co-founders actually revealing himself to the scientific community. A brave move, perchance.

Until now, PubPeer has thrived because of the anonymity involved, on the part of both creators and contributors alike, given that such critique of an established scientist's work is far from a trivial pursuit, and is not unlikely to cause real recriminations if not actual lawsuits by way of response. From the outside, people often perceive academia as this peaceful, creative ivory tower existing in its own vacuum, with almost no infiltration of the toxic mores from daily life in most other forms of business - but that's simply because that's what academia wants people and governments to believe. 

It's all about the funding, people. The public face of academia may be one thing, but rest assured it is rife with the same ruthless ambition, ego, jealousy and rage as any other typical cutthroat business today. It is a star system, with the biggest names becoming celebrities in their own right, albeit generally only inside that ivory tower, as well as inside their own heads. Nobody in the outside world has a clue who they are, and probably could care less, not least as most scientists don't produce anything in an entire career that truly impacts the daily life of Joe Public. 

So it's an insular world, its very own galaxy if you will, where the stars are stars, separate from any dark matter, and the money pours in and the experiments roll on. This system has by and large worked very well (depending on where you are placed in it, perhaps), policing itself, but the introduction of PubPeer has introduced a disturbing capacity for scientists at any level to pick apart a piece of published work or even whistleblow on the goings-on in some superstar's publication factory (i.e. laboratory). It seemed that anonymity would be the only way to go, otherwise entire careers could be put in jeopardy for publicly airing dirty laundry that has been historically kept quiet. 

Ditto for any accusations that data cannot be repeated, or worse, any claims that there was any degree of fraud involved in the publication of a certain piece of work. This gets us into the dark matter of this scientific galaxy, which PubPeer may be able to expose and likely could cause quite a bit of galactic chaos by doing so, but there is a strong argument that this would be a good thing, and could help clean up the scientific publication process. Just don't get caught doing it, if you intend to pursue a career at a laboratory bench or office! 

Given all of the above, I was quite shocked to read this week that the co-founder of PubPeer has decided to "out" himself, and reveal his identity. He is none other than a certain Brandon Stell, a neuroscientist at CNRS, in Paris. The move comes at an interesting time for PubPeer, having exceeded some 35,000 comments on their online journal club, they have now decided to reorganise the outfit as the PubPeer Foundation, a not-for-profit agency of which Stell will be the new president. 

Stell is quite open about the fact that it was fear that caused them to be anonymous, in that he didn't want his name associated with PubPeer if it was a disaster, or if the establishment turned fully against it. It was entirely possible that those involved in it would become pariahs of the scientific world and its process, and potentially be excommunicated from it due to their involvement. However, today, after some three years and considerable notoriety (including one lawsuit against it!), in order to grow and sustain itself, the outfit needed to raise money and inevitably some figurehead needed to be identified and attached to the organisation. 

No doubt the unmasking of Stell may raise some more accurate guesses as to who the other two co-ounders (known only as George and Richard Smith, respectively) may be, but irrespective of that, it is obvious that PubPeer user anonymity will not be going away anytimg soon. Stell realises that accusations of misconduct come with too heavy a price in the scientific world, which is why whistleblowing is such a rare thing, and the threat of ruining one's career is too real for anonymity to be waived. Hell hath no fury like a scientist scorned and exposed!

PubPeer has the potential to change the way science is reported and published, and may go at least part of the way to resolving the current crisis in modern biology vis-a-vis the reproducibility and actual believability of data typically published in well-respected journals. Academia does not appear to be solely capable of solving this problem, nor even acknowledging that there is a problem, so it's probably preferable that an apparently rogue outfit gets the ball rolling for them. I will end this one with the words of Brandon Stell, himself - 

"Post-publication peer review has the potential to completely change the way that science is conducted. I think PubPeer could help us to move towards an ideal scenario where we can immediately disseminate our findings and set up a different way of evaluating significant research than the current system...."