Waiting for the cyborg scientists

[This article was first written as an editorial for the October 2019 issue of The Biochemist, magazine of The Biochemical Society. The issue focused on the growing role of Applications of Artificial Intelligence in Molecular Biology].


bio04105_cover-figureFrom time to time there are innovations whose relevance catches you by surprise. I have to admit that, for me, the applications and implications of artificial intelligence for bioscience is a case in point. I consider that I am usually quite good at “horizon-spotting”, especially in areas with ethical implications, but in the case of AI I got this spectacularly wrong.

Perhaps as a consequence of watching too much science fiction, I languished under the false impression that AI was all about engineers and computer programmers attempting to develop a humanoid being. As such, I thought of AI as being primarily of interest to disciplines more closely aligned to physics. Of course this IS one aspect of work on artificial intelligence. I now know that what I was picturing would be termed “strong” AI (aka “artificial general intelligence” and “full AI”), the attempt to replicate human characteristics such as reasoning and intentionality. (From my recent reading it seems that within the AI field inclusion of consciousness in this list is a moot point, so we’ll leave that there for now).

What I had completely failed to appreciate in my casual dismissal of biological AI was the applications of machine learning to specific tasks, via the capacity to evolve rules. In contrast to strong AI, these are known as “weak AI” or more often “narrow AI”, due to the focused nature of the tasks achieved. Continue reading

Can students be mistaken about the efficacy of teaching?

At the November meeting of our Bioscience Pedagogic Research group I led a discussion of the recent paper “Measuring actual learning versus feeling of learning in response to being actively engaged in the classroom“. The study, published in the prestigious journal Proceedings of the National Academy of Sciences, was led by Louis Deslauriers and was conducted on Physical Sciences programs at Harvard University.

Slides from my summary of the paper can be seen here

The principal take-home message from the study was that students learned more from active teaching sessions, despite feeling that they had gained more from passive lectures. It was a “cross-over study” (all participants experienced both teaching methods, but on different topics) and all had the same hand-outs and slides, in either the ‘active’ or the ‘passive’ sessions. As the authors point out “The crucial difference between the two groups was whether students were told directly how to solve each problem or were asked to try to solve the problems themselves in small groups before being given the solution” (p19252). Continue reading

Putting my concerns on the Table

[This article was first written as an editorial for  the August 2019 issue of The Biochemist, magazine of The Biochemical Society. The issue focused some of the elements that play a major role in the chemistry of life ]

bio04104_cover-figureIn the August 2019 issue of The Biochemist we join with other scientific communities in marking the International Year of The Periodic Table, which celebrates the 150th anniversary of Dmitiri Mendeleev’s groundbreaking systematic organisation of the elements. As our contribution to the celebration we have a collection of features describing facets of the contribution played by several of the elements most important to the chemistry of life.

A recent visit to MediaCity, home to parts of both the BBC and ITV networks, illustrated the reason why I have a love-hate relationship with the periodic table. In ways reminiscent of the cultural appropriation of the double-helix, wider society has taken and abused the notion of the periodic table for purposes that reveal a fundamental lack of understand about its power and significance. Many people are under the false impression that the periodic table is merely a convenient way to put vaguely related things into a series of boxes. The grid on display at MediaCity, for example, was serving to advertise different components of the BBC’s output. A quick Google search also throws up “periodic tables” for beer, cocktails, iPad apps, wrestling, horror movies and even meat. Whatever your interest, it seems, some wag had authored a “periodic table” for it.

There may or may not be an element (no pun intended) of rationality underpinning the clustering of components within such grids. However, even the most logical arrangements fail to recognise the crucial dimension of Mendeleev’s original and its descendants. As most readers of The Biochemist will, of course, be aware the elegance and power of the periodic table is the predictable progression in properties associated with moving across any row or down any column. The astonishing thing about Mendeleev’s table were the blank spaces—gaps left for as-yetundiscovered elements about whose properties he was able to make accurate predictions. Subsequent research not only confirmed their existence, but also Mendeleev’s description of their characteristics.

Random things put in boxes doth not a periodic table make. So, my churlish attitude towards these faux periodic tables largely derives from what is, in effect, their black and white appreciation of Mendeleev’s masterpiece where their ought to be wonder expressed in glorious technicolor.

Now the T-shirt emblazoned “Ah – the element of surprise”, however, that IS funny.

A copy of the original article can be found via this link

Synthetic Biology: With great knowledge comes great responsibility

[This article was first written as an editorial for  the June 2019 issue of The Biochemist, magazine of The Biochemical Society. The issue focused on Synthetic Biology and appeared shortly after the death of recombinant DNA pioneer Sydney Brenner.]

Since the publication of our previous issue of The Biochemist, we have been saddened to hear of the death of Sydney Brenner (see this link for a fuller obituary). Brenner was a giant of molecular biology in the second half of the 20th Century, conducting pivotal experiments and generating insights on many aspects of biochemistry which have become the cornerstone of our understanding of how life works. These include the existence of the triplet codon for ‘reading’ nucleic acids to make proteins, the existence of messenger RNA and, prior to that, fundamental work on the structure of bacteriophage. Brenner was a pioneer in establishing the nematode worm Caenorhabditis elegans as a model organism, a decision that was to lead to his sharing the Nobel Prize in Physiology or Medicine in 2002 for “discoveries concerning genetic regulation of organ development and programmed cell death”.

In the context of the current issue, which has a focus on synthetic biology, it is also relevant that Brenner was a key participant at the famous February 1975 conference at Asilomar, California. The meeting had been organized to discuss the safety and regulation of the emerging field of recombinant DNA technology. Over 100 leading molecular biologists were present, and the consultation was conducted in the presence of sixteen members of the press. Journalists included Michael Rogers from Rolling Stone who described Brenner as “the single most forceful presence at Asilomar” (Fredrickson, 1991). Amongst Brenner’s major contributions was promotion of the concept of ‘biological containment’ alongside physical interventions to safeguard against the accidental spread of genetically modified organisms.

The technology debated at Asilomar, combined with forty years of subsequent innovation are, of course, pivotal to synthetic biology. Concerns about ‘bioerror’ as well as bioterror persist, especially when some of the intended applications (e.g. bioremediation) would require the release of altered organisms into the environment. Much of the focus of this field remains the remodelling of microbes to carry out specified function, an emphasis which is reflected in several articles in this issue. As will also be evident, however, developments are occurring in a variety of other organisms. These include altering plants to be biofactories to manufacture a chosen product, or exploiting our knowledge of molecular biology to reduce unwanted effects of protein therapeutics whilst retaining the desirable characteristics.

The potential applications of synthetic biology are extraordinary, and we are certainly only at the beginning of this revolution. We need, however, to heed the spirit of Asilomar and proceed with due caution, in case our knowledge outstrips our wisdom.

Fredrickson D.S. (1991) Asilomar and Recombinant DNA: The End of the Beginning, in Biomedical Politics (ed: K.E. Hanna). Washington DC, USA: National Academy Press

A copy of the original version of the article can be found here.

What is neuroethics?

[The following text was originally written as an editorial for the October 2018 issue of The Biochemist, magazine of the Biochemical Society. The full issue can be found here].

For many readers of The Biochemist, it will have been curiosity about the inner workings of the body, and what goes wrong in states of disease, that triggered their journey into studying molecular biology. No organ of the body is more important than the epicentre of that very curiosity, the brain. Through a variety of approaches, we are building understanding of the functioning of both the healthy and the diseased brain.

These discoveries raise a plethora of ethical questions, and represent one dimension in the burgeoning field of Neuroethics. As far back as 2002, philosopher Adina Roskies noted that Neuroethics encompassed both the ethics of neuroscience and the neuroscience of ethics. Even sticking, in the present context, to ethical issues associated with biochemistry, there are plenty of examples where dilemmas are raised.

  • If someone’s aggression is linked to possessing the “wrong” Monoamine A oxidase gene and, in consequence, they are less efficient at breaking down neurotransmitters, can they be held less culpable for criminal behaviour than someone with the more “restrained” allele?
  • As we start to understand more about the molecular changes (e.g. epigenetics) underlying the influence of environmental factors on behaviour, can it be acceptable to artificially mimic those changes in order to achieve the same (or a different) outcome?
  • Is there an ethical difference between providing Ritalin to a boy with attention deficit, in order to move their concentration more into the “normal” range, and offering the same drug to a university student hoping to avoid distraction in the run-up to an exam?
  • Is it morally acceptable to conduct brain-based research on model organisms, when the relevance of that research become more applicable to human health as the animal studied get closer in mental capacity to humans?
  • If, as an alternative, we use human brain tissue organoids in research, is there a point in their development when they are “too human” to use in this way? And would transplanting human brain organoids into rodent models be an acceptable alternative to research on primates?

A PDF of the article can be found here.

Forty years of IVF

I mentioned in a recent blog post (here) that I was intending to re-post some of the Editorials I have written for The Biochemist over the previous two years. Here is the first, from June 2018, in which I reflected on forty years of IVF in the introduction to an issue on Fertility.
The Editorial can be found here.
The full issue on Fertility can be found here.
And the text is also reproduced below

One of the unsettling aspects of growing older is the realization that events which occurred within your own lifetime are considered by others to be history. This experience struck me for the first time when one of my children was studying the fall of the Berlin Wall for their GCSE course.

2018 marks the 40th birthday of Louise Brown, the first baby produced by IVF (in vitro fertilization). For many readers of The Biochemist this pre-dates their own birth, and definitely falls into the category of history. In 1978, I was a schoolboy who hadn’t quite qualified for long trousers. I was sufficiently news-savvy to appreciate that a significant breakthrough had occurred but without being clear on the details. (In truth, I rather suspect this caveat could also have been applied to my understanding of the more traditional route to conception). In the intervening period, IVF has become the cornerstone of a broader array of assisted reproductive technologies (ART), some of which are discussed in more detail in articles in this issue.  Continue reading

Ruminating on my ruminations

BiochemistMagHomepageBoxImgAs the articles for the December 2019 issue of The Biochemist start to loiter in my inbox, I realise that we must therefore approaching the second anniversary of my taking over as Science Editor for the magazine. Doesn’t time fly when you are having fun!

It is a huge honour to have a big hand in production of this Biochemical Society publication. The Biochemist is intentionally a magazine, as opposed to a journal, and this influences the style and depth of the contents. It is hoped that all of the pieces are accessible to an undergraduate biochemist but with content that will be of interest to more seasoned academics, possibly introducing them to sub-fields of molecular bioscience that are outside their usual area of expertise. Each issue has themed features in the “front half”. In the past couple of years we’ve looked at:

  • Biomaterials;
  • Molecular Motors;
  • Fertility;
  • Food Production;
  • Molecular Biology of the Brain;
  • Immunology;
  • Biophysics;
  • Synthetic Biology;
  • Elements in Biochemistry;
  • Artificial Intelligence (forthcoming);
  • Venoms and Toxins (forthcoming)

Those who have done a quick tally will recognise that this equates to six issues per year, which represents quite an undertaking. My role as Science Editor includes: chairing the Editorial Board which, amongst other things, decides on the themes for the year’s issues; suggesting potential authors; reviewing and editing papers.

Continue reading

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