On Friday 17th April, we had great fun holding an opening event for our £8.4m MRC-funded CLIMB project and facility at Warwick Medical School.
[For those of you who wish to know more about the CLIMB (cloud infrastructure for microbial bioinformatics) project, take a look at our web site: http://www.climb.ac.uk or watch Tom Connor's talk on YouTube: https://www.youtube.com/watch?v=fZhw5FMLUjM.]
You can access a YouTube video of the first half of the event here:
The event kicked off with me providing a brief introduction to the project and stressing the achievements so far:
- spending millions of pounds on bioinformatics infrastructure within a single financial year (£3.7m on computers across the four participating universities; £0.7m on building work at Warwick and >£1m at Swansea)
- getting all the procurement, purchase orders, invoices, building etc through our university systems
- recruiting excellent support staff and academic staff to the project
- getting the building work finished (an end to all that noise!)
I then introduced our three guest speakers:
- Stanley Falkow, godfather of the field of bacterial pathogenesis, skyping in from Stanford and immortalised in our glasswork with his quote "Never met a microbe I didn't like"
- Randal Keynes, great-great-grandson of Charles Darwin
- Jon Chase, aka OortKuiper, science rapper.
Stan appeared on our huge 95 inch screen like Big Brother in the iconic Apple ad!
Stan has kindly provided a summary of his words of support for the project and event:
I am glad to add to the chorus of those who celebrate the opening of the CLIMB, the Cloud Infrastructure for Microbial Bioinformatics at Warwick.
As you know It’s an admirable enterprise that includes a consortium with Universities at Birmingham, Cardiff and Swansea,to permit a public as well as a private Internet resource, available to all in the UK
How I envy you! You are the generation of scientists who have availabile to you software, data stotrage and bioinformatic expertise to be able to track and understand the epidemics of the past, as well as the contemporary realties of the dynamics of infection and transmission of infectious diseases. You have the ability to examine the genome of the offending microbe as well as the host - including us, the human.
I am reminded by the presence of Professor Mark Achtman in this gathering at a time in 1978 when he, as well as Gordon Dougan, who was until recently Group Leader in Pathogen Genomics at the Sanger Centre, were visitors in my laboratory in the University of Washington. We were at that time able to sequence 75 base pairs a day, and analyze the results on a Radio shack computer with 16 K of RAM using a program I wrote in BASIC. I remember the thrill of my first ATG start codon! How far we have come in the past 37 years!
I can only dream about what you can accomplish in the next decade. Would that I will be here to learn of you accomplishments - of which, I may say, you can only dream and speculate about now! I always say The good old days are now!
Good luck and God speed in the adventure that awaits you.
Randal then said a few words, linking our efforts to the legacy of Darwin:
I’m here today because when Mark Pallen told me about CLIMB, I was fascinated and impressed by the boldness of the plan - managing all these fresh kinds of information with Cloud power and flexibility for all the intriguing investigations you’re now working out how to tackle. Mark suggested I might say some things for Darwin at this gathering, and I felt at once that yes, if Darwin could be with us for this opening today, he’d be fascinated and impressed. No – excited, I realised. He’d see very clearly the opportunities CLIMB presents, and he’d sense the spirit of the whole venture. He’d be eager to hear about every plan and delighted to talk. I thought that if it might mean anything for you today to hear what I can say about this point, I’d be glad to tell you here and now, for Darwin’s sake as well as yours. And why that? Because this venture is one of so many continuations of what he started with The Origin of Species, and I feel that all who join in the great effort in ways like yours are joined with him and each other in it.
Hearing about CLIMB – the technical opportunity, the resources you have to seize it with, and all the lines of research you’re planning to use it for, I think of the chain of scientists whose ideas you developing – Darwin as founding father and then Robert Koch, Ferdinand Cohn and Carl Woese among others since, each with his step forward. Each of them had some luck. He made it his opportunity and realised its potential. You and all your colleagues in the CLIMB collaboration have yours with CLIMB today.
Cloud Infrastructure for Microbial Bioinformatics. Wonderful words for an onlooker like me to understand, as they fit together so clearly and tightly for your purpose. Let me now touch on some points that I feel link Darwin with you.
The Evolutionary Factor
Mark Pallen took as his text for his Inaugural Lecture last year, Dobzhansky’s insistence that “Nothing in biology makes sense except in the light of evolution.” Looking then more closely at his Department’s special concerns, Mark showed how true that is for microbiology as a specialism. Looking yet closer today at CLIMB, he’s made it clear to me how central Dobzhansky’s point is for so much of microbial bioinformatics. One key point, it seems to me, is the speed of reproduction in microbiology with the extent of variation and selection in the process, and the significance of the changes for other organisms. It’s a truism how difficult we find it to observe evolution of macroorganisms; there are the few well-known examples, but for all other species it’s like ‘grandmother’s footsteps’ with the stillness whenever you look behind you for any movement. But microbial genomics can be a helter-skelter ride. In this area, excitingly, the often bucking process of change is a key concern, a central issue that we need to understand.
The Tree of Life
Darwin wrote in The Origin of Species that relationships between all species of the same kinds “have sometimes been represented by a great tree.” The ‘Tree of Life’ no less. He then wrote carefully, “I believe this simile largely speaks the truth. The green and budding twigs may represent existing species; and those produced during each former year may represent the long succession of extinct species. [In this way] the great Tree of Life … fills with its dead and broken branches the crust of the earth, and covers the surface [above] with its ever-branching and beautiful ramifications.” It’s important to recognize here that the essential point for Darwin when he wrote “I think” in his secret notebook and drew his first branching diagram, and for CLIMB now, was and is surely not the huge trunk of the great tree but quite simply those “ever-branching and beautiful ramifications”; Darwin’s “endless forms, most beautiful and most wonderful, [which] have been, and are being evolved”, as he ended his final sentence of The Origin of Species. “Are being evolved.” With those last three words Darwin placed his final emphasis on the ever-continuing process that is central to what CLIMB will be all about.
Four petabytes of data storage and 78 terabytes of total RAM. The need for such remarkable capacity and power follows directly from the understanding of evolution that has stemmed from Darwin’s writings with its randomness and variation, its endless proliferations and the whole global diversity of life in which microorganisms indeed excel over macroorganisms. Hearing your talk of ‘big data’ I think at once of the number of data mountains Darwin had to climb through his working life to gain an adequate understanding of the topics he was having to tackle over the range of life on earth to make sense of the factors involved in their global dimension. Especially, he would have said, the eight years he had to spend dissecting barnacles in order to prove himself to be a competent taxonomist, so that he’d be able to write as he wanted to, on species around the world and through geological time, and gain any serious attention for his views on what he found to explain their relations. For the time he took, we should remember his poor son who when visiting a friend at the age of ten was shown around the house and asked ‘Where does your father do his barnacles?’ From Darwin’s understanding of the endless variety of natural life and the infinite complexity of all the interactions it involves, he would appreciate at once why CLIMB is focussing so sharply on the scale of data storage and processing capacity it’s able to provide.
Value for Medicine
When Mark Pallen first explained the project to me, I saw at once its great interest for pure science, but when he explained about some of the investigations it is to be used for and mentioned the MRC funding, only then did I really take in its significance for medicine. Picking up on its potential for work on hospital infections and Antimicrobial Resistance, I remembered at once a point about Darwin. Not an achievement of his but his reaction to one of another person, how quickly he recognised its value for medical treatment and how strongly he felt about that value.
I have to sketch in some background. When Darwin was working on The Origin of Species, his first daughter, Annie, then ten years old, fell ill, probably with TB. He was devoted to her; he did all he could to save her life, caring for her night and day in her last illness; he was devastated by her loss, and he was deeply shaken by the doctors’ inability to identify, understand and treat her illness. Twenty five years later, in 1877 as Louis Pasteur was making the case for the germ theory of infection, a close scientific friend of Darwin’s, Professor Ferdinand Cohn, then a plant physiologist but later to become the founding figure of microbial taxonomy, sent him a copy of his journal for plant science. The issue contained the first photographs ever published of bacteria. They had been taken by Robert Koch who was to identify the TB bacillus five years later. Dr Koch had come to Cohn with his photographs of his first microscopic preparations of the anthrax bacillus, and had shown him his paper arguing for the first time that these bacilli were the cause of the disease. Professor Cohn recognised at once the great importance of his findings for medicine and the saving of life, and wrote to Darwin that Koch’s photographs showed “the least but also perhaps the mightiest living beings”. Darwin replied to him, “I well remember saying to myself between twenty and thirty years ago, that if ever the origin of any infectious disease could be proved, it would be the greatest triumph to Science; now I rejoice to have seen the triumph.” That in those words was what Koch’s achievement meant to Darwin, the scientist and the father.
I was fascinated to see Tom Connor’s explanation on Youtube of the CLIMB project, with his picture of the sequencing iceberg and his breakdown of the budget for different parts of the project. 75% for the expertise in the informatics, a critical need for the whole venture. It is fascinating to see how CLIMB users will be using together with their quantities of genomic data such quantities also of data of other very different kinds from very different sources, clinical, diagnostic, and then also population and epidemiological.
I have no scientific experience but have worked in the public sector on some matters needing careful and effective management of ranges of different kinds of information together, with gaps and inconsistencies in and between different datasets often compounding the difficulties of drawing any sound conclusions. So often, critical needs for information management just weren’t recognised by the managers and weren’t provided for. It seems to me that many people just don’t see these kinds of problems and their consequences, because they feel that information is just information and doesn’t need any managing to achieve completeness, accuracy, consistency, availability - and so meaning. People are often perfectly good with their own data simply because they know it well, but are then casual and careless about other peoples’, and when they use others’ in combination with their own, they don’t see the potholes until they realise they are stuck in one. With the range of data you’ll be using for all your range of aims, all the care you’re taking with the discipline of informatics will be invaluable for success.
Suggestions from Darwin
With all that lies ahead for you all in your work with CLIMB on today’s scientific and medical challenges, I’d like to offer from Darwin’s experience two suggestions on how to move forward. The first is an early comment of his when as a young man he was first glimpsing the power of the ideas he was fitting together on ‘descent with variation’ and ‘natural selection’, and the second is the last comment he made on research like yours before he died.
For the first suggestion, shortly after Darwin drew his first iconic branching diagram in his secret notebook, he spotted the extraordinary implication for all humans and animals and went on, “If we choose to let conjecture run wild, then animals, our fellow brethren in pain, disease, death and suffering, our slaves in the most laborious works, our companions in our amusements – they may partake from our origin in one common ancestor, we may be all netted together.” Just notice how he started that comment. “If we choose to let conjecture run wild …” Yes, with the fresh information and ideas you’ll be developing with CLIMB, choose to do just that, dare to! Bold conjectures may succeed powerfully.
Darwin’s last comment on research of this kind appeared in a preface he wrote for a work by a brilliant young friend on plants’ remarkable adaptations for cross-fertilisation by their pollinators. He spun out a series of ideas he’d found in the book for further investigations he’d love to pursue, and then, knowing privately that he was dying and wouldn’t be able to take any of them up, he continued – “But it would be superfluous to make any further suggestions. These will occur in abundance to any young and ardent observer who will study this work and then observe for himself, giving full play to his imagination, but rigidly checking it by testing each notion experimentally. If he will act in this manner, he will, if I may judge by my own experience, receive … much pleasure from his work.”
CLIMB now offers a wealth of fresh opportunities for research just like those that Darwin could then see. Opportunities for “young and ardent observers”, if they will “observe for themselves, give full play to their imagination, but rigidly checking it by testing each notion experimentally”. And we here today can add “analytically” with all CLIMB’s processing powers.
Then Randal symbolically opened the champagne
and we had a brief interlude before Jon Chase began his science rap session.
You can access the video of Jon's performance here:
A full set of photos of the event can be accessed here: https://www.dropbox.com/sh/ky3ck6wsij4mx4b/AABxsWEoVlxklGQ2NhjegzgVa?dl=0
And to close this blog post, how about this classic pose of me and Jon! Cool, no?
And a big thank you to all who worked to make this such a special event!!