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sequencing the neandertal genome Alison Campbell May 23

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I’ve had this one in my ‘must write about’ file for a little while: in the May 7th edition of Science, a large research team announced that they’d produced a draft sequence of Neandertal DNA (Green et al. 2010). Using DNA from 3 individual Neadertals, the multi-institutional team managed to decipher more than 4 billion nucleotides from the Neandertal genome. Considering that Neandertals disappeared 30,000 years ago, this is a stunning achievement.

Stunning, because DNA so old is always going to be highly degraded, & in this case the researchers were recovering fragments averaging only 200 base pairs long. What’s more, when you die the decomposers take over, & the team was faced with the challenge of distinguishing between Homo neandertalensis DNA & that from the microbes involved in decomposition. This was done by comparing the various DNA fragments with chimpanzee & modern human genomes. (Up until now just 4 fragmentary sequences of Neandertal DNA had been decoded, from loci involved in skin colour, blood groups, speech, & taste. Again, the nature of these fragments was determined by comparing them with modern human DNA sequences. The results of the Human Genome Project are not restricted to modern humans but have allowed us to look far into our past.)

Neandertals first appear in the European fossil record around 400,000 years ago & subsequently spread into Asia, as far as southern Siberia & the MIddle East. They’re regarded as the sister species of Homo sapiens. Anatomically-modern humans moved into the Middle East around 80,000 years ago & it’s long been assumed that the two species would have come into contact, then & later when sapiens moved west into Europe & also into Asia. And a question that’s often asked when I’m talking with school students is, could Neandertals & modern humans have interbred?

Up until now it hasn’t been possible to rule out the possibility. This is because, while the available Neandertal mitochondrial DNA (mtDNA) sequences fall outside the range of modern human mtDNA, this doesn’t rule out interbreeding. (If you can’t see why not, remember that mtDNA is almost always passed down along the maternal line. The absence of any mtDNA apparently belonging to Neandertals may simply mean that no female Neandertal lineages have survived to the present day.)

Green et al. extracted their DNA samples from bones from 3 different individuals, found in a cave in Croatia. (They used mtDNA comparisons to confirm that the remains were indeed from 3 different people.) And they found that yes, there probably was a certain amount of interbreeding between resident Neandertals and the new, younger species moving in from Africa. How much, is hard to say, but it appears that modern human populations from Europe, Asia & the South Pacific have 1-4% ‘Neandertal’ DNA. (But not Africa: only modern human populations moving out of Africa would have had the opportunity to meet up with Neandertals.) The authors also note that any gene flow between the 2 species probably occurred before the divergence of those modern human populations.

There’s much more to the story, though, than simply cataloguing early inter-species matings. There’s enough information in the draft Neandertal sequence to look for variants of genes that are shared by both neandertalensis & sapiens & those that are unique to one or the other. And it turns out that there are just 78 genes where a ‘novel’ variant has become fixed (either by positive selection or by drift) in the human population (although there are rather more novel non-coding sequences in the modern genome as well). Some of these are implicated in brain development & functioning in modern humans. Mutations in another gene affect the cranium, shoulder girdle & ribcage – all features where sapiens & neandertalensis skeletons differ. This is really exciting stuff, where palaeontology and genetics come together to unravel the details of a fascinating time in our past.

You can read much more about this on John Hawks’ weblog, Pharyngula (of course!), & in Carl Zimmer’s piece in Discover magazine, & there’s a video interview here on the Dolan DNA Learning Centre page.

R.E.Green, J.Krause, A.W.Briggs, T.Maricic, U.Stenzel, M.Kircher, N.Patterson, H.Li, W.Zhai, M.H.Fritz, N.F.Hansen, E.Y.Durand, A-S.Malaspinas, J.D.Jensen, T.Marques-Bonet, C.Alkan, K.Prufer, M.Meyer, H.A.Burbano, J.M.Good, R.Schultz, A.Aximu-Petri, A.Butthof, B.Hober, B.Hoffner, M.Siegemund, A.Weihmann, C.Nusbaum, E.S.Lander, C.Russ, N.Novod, J.Affourtit, M.Egholm, C.Verna, P.Rudan, D.Brajkovic, Z.Kucan, I.Gusic, V.B.Doronichev, L.V.Golovanova C.Lalueza-Fox, M.de la Rasilla, J.Fortea, A.Rosas, R.W.Schmitz, P.L.F.Johnson, E.E.Eichler, D.Falush, E.Birney, J.C.Mullikin, M.Slatkin, R.Nielsen, J.Kelso,, M.Lachmann, D.Reich & S.Paabo (2010) A draft sequence of the Neandertal genome. Science 328: 710-722 doi:10.1126/science.1188021

academic language & learning about science Alison Campbell May 03

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One of the biggest challenges faced by students of biology (or any science, really) is coming to terms with the language of science. Scientific language is precise, it’s concise, and it uses a dauntingly large number of new terms. (I saw it written somewhere – sorry, too much marking & the memory’s gone bad! – that learning the last is like learning French or some other foreign language.) Going by the conversations I’ve had with some of my first-year students, just that overwhelming number of new words can be enough to make some people seriously reconsider taking the subject. Which is kind of sad, really – & one reason why I always take a great deal of care in my lectures to introduce new terms carefully & explain what they mean & how we use them. (OK, maybe not every new word, but at the very least, the ones that I know they have trouble with.) It also highlights the fact that it’s so very important to be meticulously careful in how you use words, when communicating about science with a wider audience. While the language can add precision, its sophistication & complexity can also be a real barrier to understanding (Snow, 2010).

Catherine Snow (2010) comments that what we call ‘academic language’ – something that all university students are expected to master, albeit in the form required by their own particular discipline – tends to be concise, lacking in repetition, with a high number of ‘information-bearing’ words that allow it to be very precise, and wtih a particular set of grammaticial rules. (Most of which I break, here, on a regular basis LOL). This works just fine when you’re communicating with someone else who understands the rules of engagement, but it can be a long way from the ease & simplicity of everyday speech patterns.

Thinking about it, this is probably one of the reasons that the Cafe Scientifique movement is successful – because the organisers take care that the scientists who speak at these events are well aware that they need to present to a general audience, & to keep the jargon to a minimum. In some ways the lack fo powerpoints & so forth probably aids this, too, as it’s all to easy to fill a screen with lovely long scientific words & totally lose your audience in the process. But I digress…

Well, no, I don’t really, Because Snow points out that the habits & characteristics of oral language probably are more accessible to the non-scientist. Sentences often begin with pronouns, so the listener/reader can be drawn in  rather than held stiffly at arm’s length. Verbs really are ‘doing’ words, and if you’re getting a lot of information across, it tends to be in a sequence of ideas rather than a whole bunch of embedded clauses. (OK, I know I do that sometimes.) All too often, perhaps, a piece of written academic scientific prose can come across as impersonal, distanced, authoritative, & too full of those scary new words – this can be off-putting to newcomers, & I know from experience that it’s extremely hard for new students to produce their own written work in the same register (desirable though that may be to their lecturers). They actually need a lot of support and multiple opportunities to practice, if we want them to be able to deliver the desired standard of work on a regular basis.

And it’s not just enough to teach the vocab. This is particularly the case if the definition of a new term includes other, widely-used scientific words that the student doesn’t know either! Snow gives the example of a piece of physics text: ‘Torque is the product of the magnitude of the force and the lever arm of the force.’ Now, I have a fairly good grasp of terms like ‘magnitude’, & I know what a ‘lever’ is, so I can work that one out. But to a new student, ‘product’ & ‘arm’ & ‘force’ have other, general meanings, & if they apply those meanings to the academic definition, they will be in all sorts of strife and misunderstandings & misconceptions will almost certainly follow.

Yet students who are going to progress in science really do need, eventually, to learn to write (& speak, in oral presentations anyway) in the complex formal register of science. The devil, of course, is in the detail of how we get them there. Snow argues – & I agree completely – that this needs to be embedded in the science curriculum (ideally, before students arrive at uni, but certainly at university level). The obvious questions are, how, and what do we leave out in order to do this? (Myself, I’m not convinced that we necessarily have to leave things out, but do have to change the way we teach. Material for another post, methinks.)

And hopefully the best of those students will end up with the best of both worlds – an ability to communicate within the science community, and the skills to translate from that to the wider community beyond the walls of academe.

C.E.Snow (2010) Academic language and the challenge of reading for learning about science. Science 328: 150-452. doi: 10.1126/science.1182597

think before you write (or at least, before you hand it in) Alison Campbell Apr 26

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I’ve spent a lot of time lately marking essays from my first-year students. For many of them, this may be the first essay they’ve written in a while, & along with getting their heads around the essay-writing process, they’ve also got to come to terms with the academic environment that they’re working in. That means: making sure that they research the topic; read reasonably widely around the question they’ve chosen to work on (I always give a choice); make sure that as they write they cite the sources that they’ve used; include a properly-formatted References section; choose good-quality sources of information, & so on & so forth.

All that is probably a fairly daunting task if you’re new to the game, so I try to give as much guidance & direction as possible. There’s an outline of some of the key ideas i’ll be looking for, for example. And we give a lot of instruction, in the Study Guide & in tutorials, on things like references, proper citations, how to paraphrase, together with the really basic stuff like double-spacing, wide left-hand margins (for marker’s comments)…

Now, if you’re given that sort of support, use it! Follow instructions! I have lost count of the number of times I’ve written ‘please follow instructions’ on these essays, but overall far too many people have lost marks that they didn’t need to…

But going beyond that, it’s also necessary to think carefully & critically about the question & how you’re intending to answer it – the meaty stuff, that goes beyond issues of presentation. If you’ve been following this blog for a while, & you’re preparing for Scholarship Biology at the end of the year, you might remember me saying that a common problem for schol candidates is a tendency to do a ‘brain dump’: to write down anything and everything that might seem remotely relevant to the topic. This doesn’t do you any favours, because it does rather suggest that you haven’t thought your answer through – and skills such as critical thinking & the ability to integrate information into a coherent whole are some of the attributes that the examiner is looking for in successful candidates.

To take one of my essay topics as an example (I’ll blog about the science itself later on, cos it’s really very cool and interesting stuff): the question was based on a research paper looking at the relationship between a species of marine crustacean called Santia and the algae that grow on the animal’s exoskeleton. I asked my students to explain the nature fo the relationship and to discuss its advantages and disadvantages to the organisms involved.

Now, the relationship is essentially a symbiosis (where 2 different species live in close contact for part or all of their life cycles) or, more specifically, a mutualism, because there are advantages to both species. So the first thing I’m looking for is some definitions, and an explanation of why it’s a mutualism. But you wouldn’t include a whole lot of stuff on endosymbiosis & the origins of mitochondria & chloroplasts, for example, because that’s not relevant to the question in the form I set. (I could have asked my students to place the Santia/algal relationship in the wider context of the evolution of symbioses, but that would be a whole different ballgame.)

Similarly, once you got into discussing the advantages/disadvantages, you should be focusing on the two organisms involved in this particular example. Yes, there are a lot of other symbioses around, and perhaps fewer mutualistic relationships, but I don’t want to hear about those in a lot of detail. What you could do is point out that the whole symbiosis-mutualism thing isn’t actually all that clear-cut, and whereSantia & its carapace-dwelling algae fit on the spectrum.

But you might well include material on what closely-related species do, because the relationship we’re talking about is unique. How do other species of isopods & algae get by? What sets Santia apart? Attention to that sort of detail turns an otherwise OK essay into a very good one.

But it does require careful thought :-) So take the time to do that (yes, even in the pressure-filled context of a Scholarship exam!); it’ll repay you in the end.

what science is Alison Campbell Apr 18

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“Science can give us answers, but they are not true just because science says so. They are true or at least a usefully accurate approximation of reality because anyone (at least with training and equipment) can perform the same tests or experiments and replicate the results for themselves.”

From a commenter over at Science-Based Medicine. Says it all, really.

_________________________________________________________________________________

and also, from the same thread (different ’speaker’):

“You can have faith in religion, you can have faith in leadership, you can have faith that a treatment will help you since it is based on scientific study, but you cannot have faith in science. In science, you should only have skepticism and curiosity. The only faith that you should be asked to accept in Science-Based Medicine (which is not science), is that what has been observed in the past, will likely be observed in the present.

“You need only believe in a part of science when you repeatedly observe that part of science being correct. That belief is justified so long as you continue to observe the same results. Science should be belief in what you observe, not faith. There are questions that science cannot answer, faith can be applied to those questions.

“In a scientific argument, the better argument will lead to a better hypothesis or experiment, not to a change in policy or lifestyle. Scientific arguments are often obtuse to anybody who has not been involved in the study of a particular subject. There are many who take advantage of that obtuse nature, and use sounding sciency to sway opinion without having the data to back it up.”

live from the nz international biology olympiad training camp Alison Campbell Apr 08

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Today & tomorrow I’m down in Wellington. This year Victoria University is hosting the training camp for New Zealand’s Biology Olympiad aspirants, but I got invited to come down & help out at some of the lab classes. Which is great, because I don’t want to lose contact with the IBO organisation (or the the wider umbrella group. Science OlympiaNZ).

For me, the highlight of these training camps (which up until this year were hosted at Waikato Waikato & UniTech) is the interaction with a bunch of gifted and talented young New Zealanders. But I also value the opportunity to talk with the rest of the team of dedicated individuals who make the camps possible. This afternoon I had a lengthy session with my friend Angela Sharples, who leads the Biology organising team & is also Chair of the Science OlympiaNZ Council. One of the things up for discussion was the question: what do universities gain from their association with the movement?  After all, we’re talking fairly small numbers of students here – 19 at this year’s camp – and they’re not all going to go on to study at the host institution. And these camps do cost a lot to run, in terms of materials, resources, & staff time.

One obvious benefit is the positive impact the association has on the university’s profile with schools and teachers who are involved in the program. (Personally I think all secondary schools should be encouraging their top students to apply for an Olympiad – there are significant benefits to be had by doing so. This is probably most obvious for smaller schools, where you might have only a few students working at this level – it can be hard to find the time & resources to support them, & the students might well feel a bit isolated. If they’re selected for the Olympiad tutorial system, a whole new level of material & coaching becomes available to them, & they also become part of a wider group of like-minded students.) So even if only a few, or no, students from an IBO camp come to the host uni, nonetheless their teachers & peers will hear all about it, & that may help shape future study decisions.

But I think there’s another, & arguably more significant gain to be had for the universities. And this has to do with how well we ‘bridge’ our to the academic life of the institution. I know from Waikato’s hosting experience that the teachers involved are always very happy to talk about curriculum, assessment, syllabi & so on, and what is & isn’t available to students in their classrooms in terms of resources like microscopes & various bits of apparatus. This means that the academics involved in the camps gain an understanding of what they can expect from their students: what they’ve studied (& haven’t studied) for the various Achievement Standards; what sort of assessment practices they’ve been exposed to; & so on. (And make no mistake – there can be a real gulf between what lecturers assume about students’ prior learning, and what those students have actually done.) This can then shape what & how we teach in our first-year classrooms, which can enhance the students’ learning & also their overall experience of tertiary study. And that in turn can have a positive effect on their progression to subsequent study in a particular discipline, & the successful completion of that study. (And that, at a time when the government has signalled it’s moving to a funding model that takes completion & retention rates into consideration, is surely a significant benefit to the institution.)

And in the long term… well, I share Angela’s dream on this one. It would be great to see our top academic students valued & supported in the same way as our sporting teams. (As it is, the various Olympian movements have in the past operated on the smell of an oily rag, & their teams’ considerable successes on the world stage have been supported by those dedicated, selfless teachers who put in hours & hours of hard work for free, on top of their ‘day’ jobs – & by students’ families, who put time & effort  & money into supporting them. The Science OlympiaNZ came into being through the extremely generous and very-much-appreciated support of the Todd Foundation, & it would be wonderful if other funding bodies could also come on board.)

Given the adulation awarded to successful national sporting teams, I suspect this may require something of a culture shift! But we need our top students to take science & technology at school, we need them to study these subjects at university & go on into related careers. We have to move beyond the farm & the theme park. And while they may well go overseas at some point to continue & extend their studies – & in fact I think this is a really Good Thing – we really really need them to come back to New Zealand and continue their careers here. And – if we have a system in place that sees this happening; that recognises, encourages, & rewards studying in the sciences & in technology; that sees rising levels of science literacy across the board – then everyone’s a winner.

the costs of transpiration Alison Campbell Apr 03

One of our first-year bio labs sees our students using potometers to determine how transpiration is affected by things like light, humidity, & wind movement. Those of my readers who are school students may well have done something similar, but for those who arent – a potometer allows you to measure the rate of water uptake by a leafy shoot.

Patometer

As the plant takes up water, the level of water in the pipette falls, & so students can measure changes in water uptake over time. (This is assumed to equal the rate at which water is lost to the atmosphere – by transpiration – although a small fraction will actually be used in photosynthesis.) They also calculate the leaf surface area of their shoot, so that they can work out water loss in mL/min/m2 – & then we get them to scale it up & think about what this would look like in terms of L/ha/day. Turns out to be rather a lot.

Just how much was brought home to me when I read a recent Nature article by David Beerling & Peter Franks (2010). (Beerling is the author of The Emerald Planet, which is a great exposition of the impact of plants on the history of life on Earth.) It turns out that land plants put 32 thousand billion tonnes of water vapour into the atmosphere each year – this is ‘double the total amount of water vapour in the atmosphere’ (if that sounds strange, remember that water is constantly added to & removed from the atmosphere during the water cycle). In other words, transpiration by land plants plays a significant role in the global water cycle.

Flowering plants (also known as angiosperms, or anthophyta) have the highest transpiration rates of any plants. They are able to support this because they have a complex leaf structure that includes a network of veins distributing water to the leaf cells doing the photosynthesising. This means that angiosperm leaves have better ‘hydraulic conductance’ (ie they’re better at getting water to the leaf cells) than, say, gymnosperms or ferns, but Beerling & Franks point out that this comes at a cost to the plant because the water-conducting internal plumbing tissues are rather expensive to manufacture. They ask ‘why evolution apparently drove the selection of leaves with a capacity for higher transpiration rates despite a rising carbon penalty for construction.’

LeafVeins

The demands of transpiration and gas exchange demand something of a balancing act from plants. Plants take in CO2 for photosynthesis through stomata: tiny pores in the leaf surface, each controlled by a pair of ‘guard cells’. Transpirative water loss also occurs through the stomata. Flowering plants evolved at a time when levels of atmospheric CO2 were falling, & in these conditions leaves with high numbers of small stomata would have higher rates of photosynthesis than plants with fewer stomata. Plants with lots of stomata would maximise their CO2 uptake – but would also lose more water by transpiration. This meant that for maximum photosynthesis plants needed not only high numbers of stomata but also more highly reticulated veins in their leaves – Beerling & Franks describe this as a ‘hydraulic arms race’, driven by the availability of CO2 in the atmosphere.

I’ll be giving this paper to my students to read, when classes begin again after the Easter break. I’d like them to read The Emerald Planet as well, but we’ll start off small :-) And I’ll also recommend that they read this post about leaf venation on the Culturing Science blog. (So much good science blogging out there; I’m always stumbling across something new.)

D.J.Beerling & P.J.Franks (2010) The hidden cost of transpiration. Nature 464: 495-496

the costs of transpiration Alison Campbell Apr 03

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One of our first-year bio labs sees our students using potometers to determine how transpiration is affected by things like light, humidity, & wind movement. Those of my readers who are school students may well have done something similar, but for those who arent – a potometer allows you to measure the rate of water uptake by a leafy shoot.

Patometer

As the plant takes up water, the level of water in the pipette falls, & so students can measure changes in water uptake over time. (This is assumed to equal the rate at which water is lost to the atmosphere – by transpiration – although a small fraction will actually be used in photosynthesis.) They also calculate the leaf surface area of their shoot, so that they can work out water loss in mL/min/m2 – & then we get them to scale it up & think about what this would look like in terms of L/ha/day. Turns out to be rather a lot.

Just how much was brought home to me when I read a recent Nature article by David Beerling & Peter Franks (2010). (Beerling is the author of The Emerald Planet, which is a great exposition of the impact of plants on the history of life on Earth.) It turns out that land plants put 32 thousand billion tonnes of water vapour into the atmosphere each year – this is ‘double the total amount of water vapour in the atmosphere’ (if that sounds strange, remember that water is constantly added to & removed from the atmosphere during the water cycle). In other words, transpiration by land plants plays a significant role in the global water cycle.

Flowering plants (also known as angiosperms, or anthophyta) have the highest transpiration rates of any plants. They are able to support this because they have a complex leaf structure that includes a network of veins distributing water to the leaf cells doing the photosynthesising. This means that angiosperm leaves have better ‘hydraulic conductance’ (ie they’re better at getting water to the leaf cells) than, say, gymnosperms or ferns, but Beerling & Franks point out that this comes at a cost to the plant because the water-conducting internal plumbing tissues are rather expensive to manufacture. They ask ‘why evolution apparently drove the selection of leaves with a capacity for higher transpiration rates despite a rising carbon penalty for construction.’

LeafVeins

The demands of transpiration and gas exchange demand something of a balancing act from plants. Plants take in CO2 for photosynthesis through stomata: tiny pores in the leaf surface, each controlled by a pair of ‘guard cells’. Transpirative water loss also occurs through the stomata. Flowering plants evolved at a time when levels of atmospheric CO2 were falling, & in these conditions leaves with high numbers of small stomata would have higher rates of photosynthesis than plants with fewer stomata. Plants with lots of stomata would maximise their CO2 uptake – but would also lose more water by transpiration. This meant that for maximum photosynthesis plants needed not only high numbers of stomata but also more highly reticulated veins in their leaves – Beerling & Franks describe this as a ‘hydraulic arms race’, driven by the availability of CO2 in the atmosphere.

I’ll be giving this paper to my students to read, when classes begin again after the Easter break. I’d like them to read The Emerald Planet as well, but we’ll start off small :-) And I’ll also recommend that they read this post about leaf venation on the Culturing Science blog. (So much good science blogging out there; I’m always stumbling across something new.)

D.J.Beerling & P.J.Franks (2010) The hidden cost of transpiration. Nature 464: 495-496

a new hominin from siberia? Alison Campbell Mar 29

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ResearchBlogging.org

The latest edition of Nature carries an item that raises the possibility of another new – & recent – new hominin species, this time from Siberia (Krasuse et al., 2010). A few years ago, when the story about Homo floresiensis first broke, I remember commenting to my classes that it was probably only a matter of time until another recent relative popped up. After all, all the evidence to date shows that our family tree is much bushier than scientists used to think – when I was in high school that tree was presented as essentially linear in nature. But Siberia?

My mother used to say (when asked by importunate students how old she was), ‘I’m as old as my little finger & older than my teeth.’ In the case of this possible new hominin, that would make her very old indeed. The new find consists of a finger bone – the tip of a pinky, in fact – and the mitochondrial DNA (mDNA) extracted from it. (For ‘pinky’ read ‘distal manual phalanx of the fifth digit’…)

The bone was found in Denisova Cave, which is in the Altai mountains of Russia & which has been occupied (on & off) by hominins for around 125,000 years. The finger bone wsa found in a layer of sediment dated at 48-30,000 years ago, & which has also yielded a range of other artefacts. Krause & his team decided to see if they could extract & sequence mtDNA from the bone; they felt this was at least a possibility as the cool conditions in the cave are better for long-term preservation of DNA than the tropics. They expected that – if their extraction was successful – the bone would be from a Neandertal or a modern H.sapiens individual, on the basis of the tool assemblages from the site and the geographic range of both species.

Using 30mg of powdered finger bone (this sounds like something Macbeth’s witches would have liked…), the research t3eam were able to extract & sequence mtCNA. They then made a section extract & compared the two sequences: they turned out to be identical. The team hen checked that their sequences came from a single individual (if one bone yielded evidence of more than individual, then there could be questions about contamination). It did.  The degradation patterns of all the mtDNA fragments were also typical of ancient, not modern DNA: further evidence that the sample was not contaiminated.

The next step was to compare the mtCNA from the Denisova cave individual with sequences from  modern human mtCNA, a sample from an individual who lived in late-Pleaistcene Russia, Neandertal mtCNA, and sequences from a chimp and a bonobo. There must have been a certain amount of excitement in the lab when the results of this came out – becaue the Denisova hominin’s DNA had nearly twice as many idfferences from modoern DNA as that of Neandertals (385 base-pair differences for Denisova/sapiens compared to 202 for the Neandertal/sapiens comparison). 

This suggests that the most recent common mtCNA ancestor for modern humans, Neandertals, & the Denisova individual lived about a million years ago.There’s a certain amount of uncertainty around the dates, but nonetheless this is a long time ago. Krause’s team comment that  ‘the divergence of the Denisova mtDNA lineage on teh order of one million years shows that it was distinct from the initial radiation of H.erectus that first left Africa 1.9 million yeers ago.’  Remember, though, that we really need DNA (ideally both mitochondrial & nuclear) from more complete skeletal remains before it’s possible to ‘place’ the Denisova hominin with any degree of confidence.

Getting back to my original comment – it’s entirely possible that multiple hominin lineages co-existed in this part of the world as recently as 40,000 years ago. If the Denisova individual is confirmed as a new species, then it would have had both Neandertal & anatomically-modern humans as close neighbours in space & time. The apparent temporal overlap of floresiensis and sapiens in Indonesia may not have been an isolated event, and our family tree will then be even bushier than my teachers ever imagined :-) 

Krause, J., Fu, Q., Good, J., Viola, B., Shunkov, M., Derevianko, A., & Pääbo, S. (2010). The complete mitochondrial DNA genome of an unknown hominin from southern Siberia Nature DOI: 10.1038/nature08976

belief & knowledge – a plea about language Alison Campbell Mar 19

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I suspect that for many of my first-year Biology students, the sheer weight of new terms they come across is perhaps the most daunting thing about the course. In some ways learning biology is rather like learning a new language – with several thousand new words swamping the page (& the brain) over the course of a 3-year degree.

But there’s more than just the new words – there’s the meaning of the words to come to terms with. This is the focus of Helen Quinn’s 2007 paper, Belief and knowledge – a plea about language. There are many words where their meaning to a scientist may be quite different from what they mean to a lay person. Quinn feels, & I agree, that some words ‘are the root of considerable public misunderstanding about science: belief, hypothesis, theory and knowledge.’

‘Belief’ isn’t really a word that sits well with science. It has a couple of meanings in everyday speech. As Quinn says, it can be ‘an article of faith’ ie religous belief. Or – conversely – in the phrase ‘I believe he is coming at 5pm’, you get the meaning ‘but I’m not really sure.’ So how are we to take those news stories that begin ‘Scientists believe’? A statement like ‘most biologists believe in evolution’ could be used to claim that evolution is as much faith-based as organised religion. (I tell my students that I don’t ‘believe’ in evolution, but accept it as the best available current explanation for life’s diversity. This can engender some interesting discussions…)

But what the statement ‘most scientists believe’ means – to scientists – is that the majority of scientists are in agreement that the weight of evidence favours a particular interpretation, & that for now there’s no evidence to contradict that interpretation. Quinn suggests we should say ’scientific evidence supports the conclusion that…’ I like this – it leaves open the possibility that this conclusion could change, if sufficient evidence to the contrary comes to light. Which is a much better reflection of the nature of science: that its conclusions are subject to change if the evidence demands it. Unfortunately there tends to be a perception that scientific ‘facts’ don’t change. (Also unfortunate is the fact that if scientists do change their interpretation of the data, they’re accused of not really knowing what they’re talking about by those who don’t understand how science operates. Sometimes I think we just can’t win!) Like Quinn, I feel that as scientists we shouldn’t be using the ‘b’ word – it gives the appearance that science is ‘just another belief system.’

‘Theory’ is another word that means different things to different people. ‘I’ve got a theory about that’ really means, ‘I’ve got a hunch or an idea, a guess.’ But to scientists ‘theory’ means a well-established explanation for a large body of data: the theories of relativity, plate tectonics, evolution… These are definitely not guesses (nor are they belief systems!), but comprehensive explanations that have strong predictive power & have been tested time & time again. They are also incomplete, but that again is the nature of science. Scientific theories may well be modified if new evidence comes to hand: Newton’s laws are an example. (Quinn notes that Newton’s laws still hold, under certain well-defined condtions – they’re weren’t just thrown out when Einstein & special relativity came on the scene.)

To finish, it’s worth repeating Quinn’s description of how scientific theories are developed, because this is a valuable description of how science operates and what sets it apart from ‘other ways of knowing’:

When we seek to extend and revise our hypothetical frameworks, we make hypotheses, build models, and construct untested, alternate, extended theories. These last must incorporate all the well-established elements of prior theories. Experiment not only tests the new hypotheses; any unexplained result both requires and constrains new speculative theory building – new hypotheses. Models… play an important role here. They allow us to investigate and formulate the predictions and tests of our theory in complex situations. Our theories are informed guesses, incorporating much that we know. They may or may not pan out, but they are motivated by some aspects or puzzles in the existing data and theory. We actively look for contradictions. 

 

H.Quinn (2007) Belief and knowledge – a plea about language. Physics Today January 2007: 8-9

how biology teachers can respond to intelligent design Alison Campbell Mar 17

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Creationism is a recurring issue for teachers of biology. It can come in many forms (eg young-Earth creationism, old-Earth creationism, & so on) but – despite what many ‘IDers’ would say – its most recent incarnation is as intelligent Design ‘theory’, or IDT. (I use the quote marks advisedly; Intelligent Design doesn’t offer any evidence that can be explained by a coherent scientific theory, instead preferring to generate a false dichotomy between IDT and evolution: if evolution is wrong about ‘x’, then IDT is correct.) While IDT received a resounding defeat in the Dover trial of 2005, it continues to be promoted around the world as a ’scientific’ alternative to evolution.

Anyway, a colleague has just sent me Jim Mackenzie’s paper, How biology teachers can respond to Intelligent Design, which I thought I’d talk about here. As Mackenzie says, a significant number of authors have already argued convincingly that IDT is bankrupt as far as scientific theories are concerned. He proposes several strategies that science teachers can use in dealing with attempts to introduce IDT into their classrooms, and comments that it’s possible to use these with younger children. I think this is particularly useful given that the 2010 NZ science curriculum makes evolution an organising theme for biology (aka the ‘Living World’) from the earliest years of primary schooling. Mackenzie’s strategies are drawn from a case dating back more than 20 years, from an attempt to mandate the teaching of creation ’science’ – surely an oxymoron - in Arkansas schools. I found this a little surprising given the more recent Dover case, but then it is all creationism under the skin, despite attempts by various ID proponents to claim otherwise.

Just as in Dover, the Arkansas attempt to insert creationism into school curricula claimed that there was strong scientific evidence in support of doing so. The case went to court. In his decision, Judge Overton noted that teachers given the job of producing a curriculum for teaching biology from a creation ’science’ viewpoint could not find any scientific articles in its support. Not one. There was simply no creationism research available to make this a viable alternative to evolution.

Mackenzie suggests that teachers wishing to show that ID is outside science should use a ‘wide’ definition of science. He argues that definitions of science allowing only ‘natural’ (as opposed to supernatural) explanations are too narrow & risk being accused of excluding ‘too much’. He then goes on to state that this definition is ‘inoperative [in any case] because once an explanation comes to be incorporated into science it is seen as natural and matrialist, even if had previously seemed not to be’, & gives Newton’s theory of gravity as an example. Gravitational theory was originally viewed as magical or occult, but because it allowed accurate predications, was eventually accepted. Well & good, but the suggestion that if scientists accepted IDT as scientific, its arguments might be accepted as Newton’s were seems to me to be drawing a long bow. There are many reasons why scientists have already rejected IDT as non-scientific, as Mackenzie himself admits. It is, however, useful to emphasise, as he does, that even when the bar of what is considered ’science’ is set very low, IDT fails to clear it. There is still no ID research published in scientific journals that clearly presents evidence in support of ID (attempting to show that evolution can’t explain something, & claiming that as evidence ‘for’ ID, doesn’t count.)

The second strategy is to make it clear that religion is not the enemy of science. Part of the reason for excludng creationism from US schools lies in the constitutional separation of religion and the State. Show a particular standpoint is religious & it can’t be taught in schools in the USA. That’s not the case in many other places, & here in NZ it’s possible to present religious instruction in state schools, provided parents have the opportunity to opt out. The problem here, as recent mailouts to science departments have shown, begins when attempts are made to present a particular religous viewpoint in the guise of science. (I thought the Ministry of Education’s response to this was a bit of a cop-out: saying that parents can withdraw their children from religous education ignores the fact that this stuff was being sent to science teachers with the obvious hope that it would be incorporated into science classes.)

Nonetheless this is a key point – there’s nothing to be gained, if the question of creationism is raised in a science class, in ridiculing religion. Religious beliefs are often strongly held & denigrating them won’t do anything to convince a student (or their parents) of the validity of evolution & is more likely to set them at loggerheads with the teacher. A more useful strategy might be to point out that major religious leaders – including the last Pope – have indicated that there is no conflict between faith and science on this matter.

Mackenzie’s third key statement is that ’science teachers should trust their own expertise’ – and this means bringing that expertise to the fore. We’re all aware (or we should be!) that in science theories are constantly being tested, added to, modified. There’s much about the current state of evolutionary biology that Charles Darwin would never have recognised: Mendelian genetics, the concept of genetic drift, punctuated equilibrium, horizontal gene transfer… All these new ideas have been tested empirically & subsequently become an established part of evolutionary biology (& after that, they make it into the textbooks). There’s a very strong case to be made for us to talk about all this with our students, rather than treating it all as a fait accompli. As Mackenzie says, ‘[t]here may always be new ideas, new evidence, and every scientific conclusion is open to revision.’ How better to give students an understanding of this key aspect of the nature of science?

And finally, he suggests that ‘alternative theories should not be excluded.’ Well, I’m fine with that, as far as it goes – & as long as we are talking about ‘theory’ in the scientific sense. But what Mackenzie really means is that, faced with a request to include ID in the classroom, teachers should respond that they would intend to look at a wider range of alternative perspectives . This of course assumes that teachers are aware of that range, and are confident in their ability to explain why they do not constitute a scientific explanation for life’s diversity. And that there is actually time in the full-on classroom day to do this approach justice.

J.Mackenzie (2010) How biology teachers can respond to Intelligent Design. Cambridge Journal of Evolution 40(1): 53-67. DOI: 10.1080/03057640903567039

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