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Cod, correlation and causation

so help you Cod

 at the Guardian reports on a battle between science and politics which is worth highlighting. The Atlantic cod fisheries in the Atlantic collapsed during the 90s due to overfishing. They have yet to recover. The Atlantic cod is an apex predator and its decline effected a trophic cascade, which modified the original food web, perhaps irrevocably.

The Canadian government is holding the grey seal responsible for this. They argue that the seals, which are growing in number, are preventing the recovery of the stocks and are planning to kill 70,000 of them next year.

This has vexed a group of marine biologists at Dalhousie University so much that they wrote an open letter arguing that cod are rarely preyed upon by the seals. Instead, the cod’s main predators are other, larger fishes. And in actual fact, the seal preferentially feeds on these fishes. So any reduction in seal numbers will produce the opposite result to the one intended, seals will be killed, the predatory fish population will increase, and the cod population will decline even further.

Correlation does not imply causation. But perhaps, the view of the Canadian government is that of Winston Churchill who once remarked, scientists should be on tap, not on top.  It will be interesting to see how this one plays out.

Author

Adam Kane: kanead[at]tcd.ie

Photo credit

wikimedia commons

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Bamboo systematics: less swaying in the wind

Young shoots of Phuphanochloa Sungkaew & Teerawat.: a new species and genus of woody bamboo discovered by TCD botanists.

The bamboos are an extraordinary group of plants and the only large group of grasses to diversify in forests. They represent a major radiation in the angiosperms with nearly 1,500 species. The Bamboo Phylogeny Working Group (including TCD botanists Sarawood Sungkaew and Trevor Hodkinson) have recently used molecular, anatomical and morphological characters to update the tribal and subtribal classification of bamboos including the new genus (Phuphanochloa) shown in the photo.

Authors

Sarawood Sungkaew

Trevor Hodkinson: hodkinst[at]tcd.ie

Photo credit

Trevor Hodkinson

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A dose of Darwin

One of the more irksome aspects of life is getting sick, I always think we should be beyond this. When it comes to medicine I suppose we can ourselves lucky to be alive at a time when doctors and butchers are no longer interchangeable. But even in the 21st century we’re still engaged in arms races with bacteria and chemical warfare with cancer (military metaphors are never in short supply) . Bacteria evolve resistant strains to our best antibiotics and tumours do likewise against our attempted cures. Less grave but still illustrative is the perennial persistence of the common cold. Illness comes in many forms, wellness only one. The main problems we face in trying to create cures is that all pathogens are evolving and to realise that we too have evolved. We often end up using static measures against dynamic problems.

That said, I think this century will see some considerable advances in medicine owing to the increasing use of evolutionary insights to combat disease. This is the science of evolutionary medicine.

Some of the symptoms we most associate with being sick like fever, pain, nausea and vomiting aren’t from the disease per se, but the body’s defences in action. Randolph Nesse, who wrote the book on evolutionary medicine, says that medical doctors would do well to recognise our evolutionary origins when treating their patients.

Our biology is playing catch up to our cultural advances and this lag period can explain many modern afflictions. Nobody reading this suffers from prolonged periods of hunger but we still stuff our faces when we get the chance. Of course, before modern civilization our next meal wasn’t always a sure thing, so gorging when the going is good was the way to go. The upshot of this is a significant proportion of the developed world is obese.

Some of the ideas of evolutionary medicine seem to run counter to our regular approach and our intuition. For instance, when treating a patient with chemotherapy, we use the most potent chemicals and this seems perfectly reasonable. We want to hit the tumour hard and fast. In fact, all we do then is put a strong selective pressure on the tumour cells to evolve resistance, ultimately shortening the patients’ lives. Instead, we should only give the minimum dose necessary to keep the cancer under control.

Fleming’s discovery of penicillin is one of those instances of serendipity that turned out to be a great boon for medicine. But I’d prefer not to rely on serendipity if you don’t mind! It would be far preferable to know why how and why diseases arise. Bernard Crespi is doing this with his research on schizophrenia and autism. Crespi argues that these disorders are diametrically opposed, autism is the result of an underdeveloped social brain whereas schizophrenia comes from a hyper-developed one. They are caused by the abnormal expression of imprinted genes, i.e. ones expressed according to the parent they came from. If true, then we can use opposing treatments to treat these twinned disorders.

Unfortunately, as Richard Dawkins puts it, we evolved to be fecund not necessarily to be healthy. Any competition between the two and the latter won out. But now at least we know that’s the case and we can do something about it.

Author

Adam Kane: kanead[at]tcd.ie

Photo credit

Dr. Barbara Natterson-Horowitz

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Biodiversity in Our Lives

It’s worthwhile highlighting the recent success of the “Biodiversity in Our Lives” campaign which has generated some notable publicity this week in Science. PhD students here at Trinity College decided to impress upon the public some facts about biodiversity and how it can impact our lives, often in surprising ways. To do this they decided to create a series of beermats which have succinct descriptions of these impacts. Pubs around Dublin have received a second round of the beermats and to coincide with this many of the students are giving pop up pub talks.

Author

Adam Kane: kanead[at]tcd.ie

Photo credit

Biodiversity in Our Lives

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“Toxic” nectar and pollen in an invasive plant species

For the longest time floral nectar was considered to be made of two components: simple sugars (such as sucrose, fructose and/or glucose) and water.  Research carried out in the past two decades however has repeatedly shown this paradigm to be incorrect.  As analytical techniques such as high resolution GC-MS and HPLC have become commonplace, the composition of floral nectar of hundreds of plant species has been investigated in detail. The findings of this research have revealed that floral nectar has a lot of components other than sugars; amino acids, lipids, proteins, and vitamins have been detected at low concentrations.  One surprising class of constituents of floral nectar has been found in plant species belonging to over 21 different families; plant secondary metabolites.  It is strange to see these secondary metabolites- compounds such as alkaloids, terpenes, and phenolics- in floral nectar because we normally associate them with defence of plants against herbivores.  They are often repellent to insect visitors and can potentially cause floral nectar to be unappealing to flower-visitors.  The paradoxical phenomenon has many potential adaptive and non-adaptive hypotheses (see Adler 2000 for an excellent review) and it’s a subject about which there has been some really exciting literature published lately.

At NERD club one of our discussions focused around this topic of “toxic nectar”.  I study the toxins found in the floral nectar of Rhododendron ponticum, a group of compounds called grayanotoxins.  R. ponticum is invasive in Ireland and I am particularly interested in the effects of these toxins on native Irish insects that may use this mass flowering resource in early spring.  Our discussion ranged from thinking about work done in other systems in which plant toxins might play an important role to considering trophic accumulation and mechanisms by which organisms deal with ingestion of toxins. I enjoyed the meeting immensely and it made me reflect upon how useful it is to discuss your research with as many people as possible.  The varying opinions and perspectives that colleagues form different departments can bring to the discussion are both insightful and inspirational.  We get so involved in our own research it is refreshing to hear these different perspectives, so thanks to everyone who could come along!

Author

Erin Jo Tiedeken: tiedekee[at]tcd.ie

Photo credit

Erin Jo Tiedeken

 

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Thinking small to think big

Charles Darwin Bacteria (Serratia marcescens), Nutrient Agar, Petri Dish

The concept of using bacteria and other microbes to test some of the big questions is creeping more and more into the world of ecology and evolution. Evolutionary biologists have been coming around to this idea for many years now (see Lenski’s experiment for a wonderful example of this) but the concept is still hard for most ecologists, particularly empirical ones to swallow. This is primarily a function of the microbial systems being thought of as ‘too simplistic’ and ‘unrealistic’ to apply to real world populations. In a review in 2009 Angus Buckling and colleagues very elegantly address the above charges and some of the other most frequently raised arguments against using bacterial microcosms.  My argument (and his!) essentially comes down to two things:

1. Ecologists are supposed to be devising models and experiments to understand the dynamics of real world populations and the consequences of anthropogenic impacts on the organisms that inhabit the planet and yet they are largely ignoring the biggest Kingdom of organisms-Bacteria!

2. While nobody is suggesting that what happens in a 200ml microcosm tube will perfectly mimic or predict the exact response of a 200acre coral reef, why can they not be used as models to help test some of the theories or predictions that might equally affect larger systems?

Microbial systems have very similar dynamics to most other empirical food webs, in particular aquatic ones with highly size-structured predator-prey interactions, social cooperation and complex community networks. The importance of bacteria and microbes in the environment and their role in disease is undeniable and widely recognised meaning that individually bacteria are some of the most well studied organisms out their in terms of their genetic information and growth patterns. This can be used to the advantage of ecologists and evolutionary biologists by isolating strains of particular interest and culturing them very easily in laboratory conditions over short time periods to yield potentially very powerful results when viewed at the population or community scale.

One of the big problems in the field of ecology is linking empirical and theoretical study results; they frequently disagree due to the time scales, interactions and networks involved. The problem is basically that, however good the theoretical model, it cannot encompass all of the complexities of a natural system, and, similarly, while the empirical studies are more difficult to rebuke for their lack of realism or complexity, it is often impossible to disentangle the many different interactions taking place to get to the root of the question. What is therefore needed is a means to bridge this gap and provide logistically feasible model systems for testing more generalized ecological and evolutionary theory. I think the microbial systems might be a partial solution to this problem, as well as being fascinating for their own sake they can really aid in the developing and testing the drivers and disentangling the complex interactions in ecological and evolutionary processes. What they lack in size they certainly make up for in potential!

Author

Deirdre McClean: mccleadm[at]tcd.ie

Photo credit

Zachary Copfer: http://sciencetothepowerofart.com/

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“See you later, pollinator”

Scientific conferences can be a great way of meeting people, getting and sharing new ideas, and networking with people from, often, all over the world. And they can be good fun too! On October 25th-28th several people in the School travelled to Norway for the annual conference held by the Scandinavian Association for Pollination Ecologists (SCAPE). This meeting is held for ecologists working with pollination, plant reproductive biology and other related fields and it attracts a small but expert crowd from Scandinavia, Europe, and sometimes even further afield (this year there were attendees from Brazil and Israel!). Continue reading ““See you later, pollinator””

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The scariest object in my office

As it is Hallowe’en season, I thought I’d write a blog post about the scariest and most horrifying object in my life at the moment – my To-Do list. This monstrous beast lurks on my desk full of tasks ranging from the mundanely specific like “write reference letter for student X” to the vague and rather more time consuming “write paper on Y”. Inevitably some of the things on the list will never get done and will slowly drop off the list like the withered limbs of a leper (I regularly re-write the list to make sure I don’t forget anything important – and also to have the satisfaction of crossing off “write list”). Others, like teaching, will get done but not until the last possible minute. I try to look at it as little as possible to avoid scaring myself into total inaction.

I would love this post to be an amazing revelation about how to make the list get magically shorter, but unfortunately the only option seems to be actually doing the things on the list (or delegating them to someone else)! Instead I decided to analyse my list to see where I am – or should be – spending most of my time. Unsurprisingly teaching makes up a good chunk of it, followed by admin and then finishing up papers from my post-doc! But after looking at the things I spend huge chunks of time on, I looked at the things that take just an hour or two hours at a time. I realized how many of these items fell into the category of academic altruism.

I think of academic altruism as doing anything in academia that helps others but doesn’t directly help you. Reviewing papers is a really obvious example. The recent controversy over academic publishing and open access has thrown this problem into the limelight, and many people have come up with excellent solutions to the problem (for example Jeremy Fox and Owen Petchey’s excellent “Pubcreds” idea). But academic altruism is far more than just reviewing papers. We all help students and colleagues by commenting on manuscripts, discussing ideas, helping with analyses and promoting each others’ papers. PhD students do this as much as (and perhaps more than) faculty members. Those with skills in data analysis (and the patience to help novices) tend to end up doing this even more than everyone else (apologies to Luke McNally who spent 2 hours teaching me MCMCglmm last week for no academic reward apart from my eternal gratitude!).

I think it’s fairly obvious that academic altruism is not generally good for career progression. Of course there may be occasions where we gain collaborators or authorship on a paper through helping others. But mostly academic altruism takes up time with little return for our time investment. That’s not to say that I think it’s a bad thing. In fact, interacting with others in this way is part of what I love about science. But there must be a cost to those who do this a lot, and a benefit to those who refuse to engage with others. Although I’m sure hiring committees like to hear about the extra help you give others, I doubt they would rate that higher than the extra high-profile papers you could have written if you were more selfish with your time. Research also tends to suggest this cost is higher for female scientists because we associate more with “caring roles” (or as our HoD puts it – “we’re less able to leave a student crying in the corridor”).

Open Access week has led to a lot of discussion of altmetrics, so what about a metric for academic altruism? Could we think of a way to do this? Could we get colleagues, students or the scientific community to rate our “selflessness”? Do hiring committees consider these factors, or do extra papers trump everything else?

Well there’s something to mull over this evening as you hide from Trick or Treaters with the lights off. And now I can go back to my To-Do list and cross off “write blog post”. Yay!

Author

Natalie Cooper: ncooper[at]tcd.ie

Photo credit

wikimedia commons

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Consciousness cut down to size

Adam Kane recently wrote a blog post on the problem of consciousness. I disagree with most of what Adam said so thought I’d write a reply post.

Adam’s post smacks of a dualism that has persisted since the earliest musings on the problem of consciousness. In essence dualism is the claim that mental processes are in some ways non-physical, that there is a “ghost in the machine” so to speak. In my opinion dualism has been one of the most obstructive and damaging ideas that philosophy has ever produced, with a pervasive legacy that can be seen in concepts of human superiority, and in the justification of inhumane treatment of animals. However, that’s an issue for another day.

For me, Adam’s conclusion of dualism does not follow from his arguments:

1. Let’s first take his example of Chalmer’s thought experiment of automaton-like zombies. Such zombies are logically possible. However, this possibility doesn’t imply dualism. They would imply dualism if they were actually physically identical in every way to a conscious individual, including the exact wiring and firing of their neurons. Whether an exact physical replica of a conscious human could be unconscious is an empirical question. Simply posing the question does not provide one iota of evidence for dualism, it simply shows that dualism is logically possible. That there really are invisible turtles sitting in all our heads controlling things is also logically possible! Now let’s consider the more restricted case where the exact wiring and firing of these zombies neurons is not identical to ours, but they are for all practical purposes indistinguishable in their behaviour. We then have a problem over how natural selection could have favoured consciousness. However, this again does not imply dualism. Consciousness does not need to be adaptive to be physical. It may be a by-product of selection for information processing, i.e. a spandrel. It is obviously a fallacy to claim that because snail’s brood chambers (the classic example of a spandrel) arose non-adaptively that they are not physical. To explain the evolution of consciousness is definitely an unresolved challenge, but this challenge does not imply dualism.

2. Adam’s argument that neurons are made of the same stuff as heart cells, and therefore aren’t the key to consciousness is a misunderstanding of how neuroscience searches for correlates of consciousness. An individual neuron may not be that special but they are collectively unique as cells in that they are connected in neural networks of mind-boggling complexity. We don’t yet have anywhere near the computing power to simulate what the human brain does, so its computational capacities are currently unknown, but definitely huge. Neuroscience is a field still very much in it’s infancy, and I have little doubt that it will begin to shed light on how consciousness is achieved over the next few decades. Hopefully gaining more insight into the how will stimulate more evolutionary biologists to tackle the why.

Consciousness is a hard problem, but it being physical should be our null position. History has shown that explanations based on non-physical phenomena have fallen time and again under empiricism’s mighty sword. As such, our priors for the how and why of consciousness should be heavily skewed towards the physical.

Author

Luke McNally: mcnalll@tcd.ie

Photo credit

Wikimedia commons

 

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Zombies and the problem of consciousness

Seeing as it’s Halloween, I’m going to play devil’s advocate with the help of some zombies and explore the Gordian knot of consciousness. I think most scientists would hold a physicalist view when it comes to their view of how the world ‘really’ is. That is to say, objectively speaking, all there is to the universe are the various interacting fields and particles of physics. The problem with such a view is that our conscious selves prove very difficult to incorporate into this picture. We are subjective beings. Finding out how consciousness came about is known as the hard problem of consciousness.

David Chalmers, a philosopher of mind, formed a clever thought experiment to illustrate the difficulty. Okay, so imagine a world where everyone has the outside appearance of being conscious, for instance they laugh when you tell a joke,  shirk away from pain, gaze at sunsets etc., the only difference is that they have no internal subjectivity, they’re automata or zombies. I don’t see any problem with conceiving of such a place, so it looks like a possibility. But if these automata are indistinguishable from us on the outside in terms of their behaviours and actions then evolution won’t be able to distinguish between them and us, so why consciousness? It looks like an unnecessary extravagance. It also suggests that there is something more to the world than the physical, because our world isn’t like that, we, or at least I, know I’m conscious.

It seems to me that our theories as to how and why consciousness evolved have fallen short in their efforts. A lot of work is dedicated to finding the neural correlates of consciousness, but that doesn’t get us anywhere! Neurons are made up of the same material as the rest of the cells in our body, but heart cells don’t generate conscious beings so why treat neurons differently. So we’re really left with two questions. How do physical things generate subjective thought? And once we get there, why is it advantageous to be conscious? It’s called the hard problem for a reason.

Author

kanead[at]tcd.ie

Photo credit

wikimedia commons