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Posts Tagged blog blogging

Sequencing the tuatara genome David Winter Jun 17

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Things have been quite around here for a while. Largely for the typical boring reasons, the pressure to get work done and on to journals that might publish it leaving little spare time. On top of that the non-science time I’ve had lately has taken up by what I think will be a  very important piece of science communication: a blog documenting The Tuatara Genome Poject.

I’ll keep trying to find time to share my thoughts here, but I really encourage all my readers to read and follow the tuatara blog – we’re going to be discussing everything from why we’d want  to sequence a genome, to actual process we’ll use to it and some of the results that we’ll gather. I won’t be writing every word, in fact, one of the goals is to get the researchers on the project to describe their work in their own words. Hopefully we’ll all learn a bit about reptiles, genome sequencing bioinformatics and a whole lot more.

Elsewhere David Winter Jan 31

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A couple of links that might be of interest for readers of The Atavism:

All the media! David Winter Sep 25

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Oh, hi there. Yeah, it’s been a while h’uh? Just been crazy busy lately you know – one thing after another with manuscripts and datasets to analyse, then I got a whole bunch of lab reports to mark. We should totally like, get back to writing/reading about science though. I’ll put something up in a bit and…*

So, things have been a little quite here lately. That wasn’t a plan to have me an that ridiculous hat up on the front page for a few weeks – just the result of having little spare time. As it turns out, a few things that might be of interest to readers here have been published over that fallow period, here’s the links:

  • I’m in a book! As I related last year, my post on the partulids land snails of Society Isalnds was selected for The Best Science Writing Online which is now available from all good book sellers. I’m ridiculously excited by this. There is also a short review in The Listener 
  • My latest little piece for stuff.co.nz deals with Colin Craig and his idea that research tells us sexual orientation is a choice, and that this is relevant to marriage equality. 
  • I was on the radio – an hour of talking about science, peer review and skepticsm on Radio One, the student radio station.

I guess to complete the set I’d need to make a TV appearance, though I can’t see that happening!



*For people with whom I’ve had exactly this conversation lately – it’s true, I have been busy, I am a terribly friend and we will catch up soon!

Graduation, nerd blogging and a talk David Winter Aug 28

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The most dedicated readers of The Atavism may have noticed a few Sundays have passed without celebration of a spineless creature. Well, you know how blogging is sometimes. A few of the things that have kept me from blogging might be of interest to readers here. This weekend was dedicated to the wearing of silly hats, posing somewhat awkwardly and the conferring of my PhD. It was almost a big enough event to make me wear a tie:

So far I’ve rested the urge to change the name that appears under these posts to Dr David Winter, we’ll see how long that lasts.

I’ve also been working a little on some more software for evolutionary biology. Since I very much aim this blog at a lay-level, and there is no reason on earth why a lay-person ought to care about the computer programs scientists use to collect and analyse their data, I’ve decided to set up a dedicated nerd blog. The first post their introduces an R library that can help researchers quickly download data from molecular biology and medical databases.

Finally, I should say their probably won’t be a new post here this weekend either, as I’ll be at the New Zealand Skeptics Conference, right here in Dunedin. I’ll be giving a talk about how the the creation-evolution “debate” as it usually plays out has very little to do with evolutionary biology, and how getting past popular misconceptions about the way evolution works makes most creationist objections to evolution into non-starters. I’ll also say why I think good old fashioned creationism is a more respectable position than “intelligent design”, so that ought to be fun. If you’re in Dunedin you can still register for the whole meeting, my talk is on at 9:50am on Saturday in Archway 3 (the best, and perhaps only, way to find this lecture theatre is to walk into the Archway building and wander around opening doors at random).

Kiwis blogging about evolution David Winter Nov 29

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As any regular readers here may have noticed, my plate is pretty full at the moment. All you are likely to read here for the next little while are quick photo-centric posts about bugs and maybe a few results of my recreational statistics (I know, it’s an illness really) on the New Zealand election.

So, if you are looking for some meatier posts about evolutionary biology and the like, you might want to know that there are a couple of other New Zealanders out there writing on these topics.

Paul McBride is a PhD student from AUT who blogs at Still Monkeys. Paul works on understanding how the ecological setting of a group’s evolution can effect the patterns and rates of change observed in that group. So far, his evolutionary blogging has mostly been about junk DNA and the ways in which we know many of the sequences in genomes serve no particular purpose.

I particularly liked finding out that Susumu Ohno had provided a theoretical argument as to why most of our genome would prove to be useless way back in the 1970s -just as the first genetic sequences were being read in labs. You can add Ohno’s insight to Haldane’s estimate of the human mutation rate (before we knew what a gene was made of!) and Nei’s use of the theory of segregation load to show that most observed genetic changes must occur without the help of natural selection and start to see the wisdom of the elders of population genetics! (Paul also blogs about beer, which suits me, and reminds me to add a post about the science of brewing to my todo list).

Jarrod Cusens is a Masters student, also at AUT, and he blogs at of trees birds and other things. I gather Jarrod’s research is at the hub of evolution and ecology - specifically looking at how to some habitats end up playing host to diverse, species-rich assemblages of organisms while others are dominated by a few species.

Jarrod’s recent posts include a look at a couple of schools in New Zealand who have given up the (very good) biology curriculum in favour of biblical creationism (including one, I’m said to say, in my turangawaewae), a profile of one of the birds that make the New Zealand spring, the shinning cuckoo, with a bit more of the cuckoo’s special brand of parasitism and a whole bunch of quotes.

So, be sure to add Paul and Jarrod to your favourite feed reader, and if you know of any other kiwis bogging about evolution and ecology let met know in the comments.

Sunday Spinelessness – Updates David Winter Dec 19

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I’m going to round out Sunday Spinelessness for 2010 with a few updates from the creatures that have featured here over the year. But, since this is going to be last post here till the first week of January or so, I’m going to start by taking just a moment to wish everyone who has commented on, linked to, tweeted about or just read The Atavism this year a merry Christmas and an enjoyable break over the new year. I enjoy writing these posts for their own sake, but it’s much more satisfying to be part of a community (no matter how small a part!) of people that are interested in the same ideas I am. Thanks.

Right, now own with the spinelessness. The little green spiders I’ve been following, and sacrificing in the name of science are still going strong. Since the last time I wrote about them I’ve seen them grab prey for the first time (confirming the suspicion that they are ambush predators) and seen males fight for the right to mate with a female. Sadly, I didn’t photograph either of these events (well, not in a way that I’d want to show other people, but there are descriptions of each tucked away in my notebook). I can, however, show you the result of those matings. About three weeks after the first one I started spotting these across the agapanthus:

At last count there were about five separate leaves sporting one of these egg sacs and a watchful mother. One very dedicated mum-to-be actually has three on the go at the moment!

I’ll have to wait a while to see the next generation of the little green spiders, but the leaf-veined slugs that featured along side them here have already moved into the next stage

I haven’t seen a full-sized slug in a long time. But these immature ones are out and about every evening, I’ll have a little more to say about them in the new year.

The pittasporum “pysllids” are still dancing, but no longer at plague proportions. There’s no respite for the pittasporum though, now it’s being devoured by leaf roller moths. If I cared more about the tree I might spray it with insecticide but while its pests are feeding animals as wonderful as this spider (anyone have a clue on an ID?) I’m happy to let them have it:

Finally, the bumblebee nest at the bottom of the garden appears to be enjoying the run of hot weather we’ve had here. Some of the bees in our backyard (no necessarily the ones that live at the bottom, since bumble bees can forage several kilometres from their base) have taken up a slightly odd habit. On a couple of warm evenings I’ve popped outside and found bumblee bees asleep inside foxglove flowers:

No doubt the little tubes make a nice warm place for a worker to spend the night if they are caught out too late to make it home. Apparently males, which are only produced towards the end of summer, will often do the same trick once they’ve left the nest and are spending their daytime waiting for a virgin queen to pass by. I think we really have to end with a bumble bee bum sticking out of a flower:

A year of Sundays David Winter Oct 24

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It’s been as close to a year as we are going to get since I posted the first Sunday Spinelessness. I wasn’t quite sure that I would be able to keep up the weekly schedule when I started the series, but I’ve managed it minus breaks over Christmas and for my trip to the USA and Canada (there are occasionally times I try and stay away from computers). Part of the reason I called the first post Sunday Spinelessness was to guilt myself into writing at least one post a week, and as I’ve moved more and more into writing up my own research over this year these Sunday posts have been a really welcome break (and a good writing excercise at that). As you can tell, I’ve been in a slightly reflective mood thinking about this post, and when I get reflective I like to look at some data.

Like, how representative has these Sunday Spinelessness posts been? The phylum is the highest level of classification within a taxonomic kingdom, animals placed in different phyla represent fundamentally different designs for life and in the order of 600 million years of independent evolution. In day to day life we probably only aware of a few phyla, vertebrates make up the bulk of Chordata, insects crustaceans and spiders are all arthopods, snails and clams are molluscs and earth worms are annelids. Depending on who you ask, and when you ask them, there are 36 animal phyla ( the confusion mainly caused by strange animals with almost no useful characters for taxonomists to look at). So, how may have been represented here:

Click above to see a larger version, note the x-axis is on a log-scale and number of species is number currently described

I knew I mainly wrote about arthropds, but I’ve only written about about 6 of the 36 animal phyla? It looks like I have a lot more work to do. Some of the phyla I’ve so far neglected are fascinating creatures;there are probably hundreds of thousands more nematode species that currently described and one of them is an important model organism in cell biology, echinoderms share some fundamental aspects of their development with vertebarates but end up being radically different (with five-fold symetry rather than our “down the middle” two fold symmetry), brachiapods look a lot like bivalve molluscs (clams and oysters and the like) and were once many times more common than their look-alikes but are few and far between now, tardigrades might just be the coolest animals on (or indeed off) earth. Even more excitingly for me, there are phyla in there I know almost nothing about. Apparently, Rhombozoa means “lozenge animal” and this phylum is restricted to parsitising the renal gland of squids and octopusses, and phoronids are worm-shaped but have a gut that loops back towards the mouth, and so on it goes.

Ok, so I haven’t really touched on the true diversity of life without a backbone yet. What about the numbers, about three quarters of these posts have been about arthropods which represents the avaliability of photographic subjects in my bakcyard but must over-represent these creatures as a whole? I came up with an index to display how representative a phylum’s post count is here. You should probably just skip to the graph which is pretty self-explanatory, but if you wanted to know the formula is

representation = log ( (speciesphylum / speciestotal) / (postsphylum / poststotal) )

And the graph:

So, arthropod species actually make up even more of the biological world than they do posts here (and just one post about peripatus is enough to make Onychophora the most overrepresented group of all). I also have to feel a little shame as a dilettante malacologist that I haven’t spoken nearly enough about the molluscs thus far. There is another post on the way with those leaf veined slugs which should help tip the balance though.

Well that’s about it. A quick look at the data tells me I’ll have no trouble finding subjects for future Sunday Spinelessness posts and I can be a little less concerned about featuring so many arthropods!

Just trying to put the punk back into punctured lung David Winter Aug 18

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I’m going to be spending the rest of my week keeping up with my real work. Neither science nor the internet have chosen to rest while I catch up with that, so there are lots of interesting things happening that you should be reading about.

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First, there’s the news that from the New Zealand Medical Journal that a woman developed a pneumothorax (air on the lung) following an acupuncture treatment. As Darcy says in the linked article, the best scientific evidence says that acupuncture performed by people who think they are redirecting the flow of ineffable forces with their needles is no more effective than someone prodding people with sharp things where the eff ever they want. There might be a small benefit to having acupuncture, but it’s a placebo effect. At the same time, and the present study notwithstanding, the risks associated with acupuncture are relatively small. Which all raises an interesting ethical question: should doctors send their patients to acupuncturists. Obviously treatments that have been shown to work better than a placebo should be the first tack, but if they fail is it OK to knowingly make use of the placebo effect? I don’t think it’s as simple as it might seem, after all acupuncture can cost a lot of money. Just as it must be a breach of trust for pharmacists to sell small vials of water to patients and call them “homeopathic remedies”, surely it’s wrong for acupuncturists to take money from patients to pay for their specialist skills in a bogus medical system? Perhaps some of the placebo effect would be down to the idea that the practitioner is steeped in some mystic art, put even if a quick in-clinic sham acupuncture session wouldn’t to the trick other placebos treatments might, without incurring the risks associated with acupuncture (no matter how small they might be). Whatever you think, you should leave a comment on Darcy’s post because he’s just become a father! (It seems his place in life has finally caught up with his sense of humour)

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There’s lots of Science (yay) and Technology (meh) on the TV this week. Media7 is having a special episode on communicating science with a panel featuring Peter Griffin and Rebecca McLeod from the scibog crew. They had a show on a similar theme last year, so it will be interesting to see if anything has changed since. Our local climate cranks certainly haven’t become sensible in the interim, but the media does seem to give them a little less room to be stupid so that’s something .TVNZ7 also has the first episode of their new sci-tech show Ever Wondered? online. I have to admit that I haven’t actually got around to seeing that yet so I can’t offer much more than the fact that its there.

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Last week I had my first crack at teaching a lab. I’ve done plenty of demonstrating before, which I’ve always enjoyed (even the lab that’s mainly about ripping the heads off Drosophila larvae) but being in charge of the whole show it something else entirely. In the end I had fun, and I think the students went away happy but I have to say I wasn’t prepared for the terrifying sea of blank or anguished expression that stared at me when I turned round from explaining something too quickly. So, I asked an award winning lecturer and her crew what they’d do if they faced that terrible sight, you can read the answer here.

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left and right handed snail shells

Did you know that snails can be right- or left-handed? In most individuals of most species the shell coils in a “right handed spiral” so when a the shell is placed “apex up” the opening (the aperture) is on the on the right hand side (like the shell on the right above). In a very few snail species most individuals are left-handed. In both left- and right-handed species you get a very few individuals which coil the other way but that pattern usually doesn’t persist for any length of time because right- and left-handed shells tend to get in each other’s way during mating. It’s even been suggested that the reproductive isolation caused by right- and left-handed snails might be enough to help with the generation of new species (I don’t know if anyone has ever looked at the distribution of chilarity among closely related snail species, but it might be interesting). Now, Kevin Zelnio has the story of a landsnail species that maintains an even number of right- and left-handed individuals, and just how it manages that.

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I’ve been reading In Pursuit of the Gene by James Schwartz which is a really well written history of the discovery of genetics. It’s reinforced my notion that statistics was entirely invented by evolutionary biologists; Galton, Pearson (of the correlation coefficient) and Fisher were all trying to understand evolution in developing their methods. I also like the strange coincidence that Hugo de Vries developed what turned out to be a poor theory of evolution based on a misunderstanding of heredity from his observations in the evening primrose. Evening primrose’s scientific name is Oenothera lamarckiana, a name which honours French biologist Jean-Baptiste Lemark who has gone down in history as someone whose mistaken ideas on heredity lead him to present a flawed theory of evolution.

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And finally, a couple of posts from here have featured in blog carnivals lately. So, go tuck in to something spineless at the Birders Lounge or read about the history of science’s frauds failures and fools.

Memorialising my own folly David Winter May 05

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I’m usually a pretty cautious kind of a guy. I might be physically incapable of proofreading but I at least think these posts through and make sure I’m not committing any grave errors of science before I hit the publish button. Usually.

A couple of weeks ago I made fun of Garth George because he underestimated New Zealand’s carbon emissions by some staggering amount. It turns I overestimated the degree of Garth George’s underestimate. Or to put it another way, I screwed up that maths. Garth George is still spectacularly wrong, out by a factor of 375 000, but I had said he was out by about eight times more than that. In putting the graphics together I’d written down the inverse of George’s error (about 2.75 millionths, or 2.75 x 10-6) to help me calculate the sizes for each triangle and when it came time to write up the post I mistook my notes, reading 2.75 x 106 or 2.75 million.

That’s not an excuse, it should have been obvious to me, as someone who passed 3rd from maths, that 3.7 x108 couldn’t be millions of times bigger than 1 x103 and in writing the post I should have caught it. It’s all very embarrassing, but if you are going to make fun of people you have to be prepared to be treated in the same way. So, in that spirit, here’s the magnitude of my error plotted for all to see:

And the worst bit, Garth George is still among the wrongest people in history but not quite on the same level as the Young Earth Creationists (and will no doubt be overtaken by Bill Gates at some stage, if he really said that thing they say he said):

Any physical science types reading this post might want to make a joke at the expense of biologists now, can I suggest this one:

A group of biologists and a group of mathematicians meet each other at a train station on their way to a conference on ecological modeling. The biologists each line up to buy a ticket, while a single mathematician collects a few coins from each his colleagues and buys a single ticket. Both groups board the train and before the biologists can ask what the mathematicians are up to one of them yells out that the conductor is on his way. The mathematicians leave on mass, cramming into one bathroom. The conductor arrives and clips the ticket of each biologist before knocking on the bathroom door and asking ’tickets please’. The mathematicians slide their single ticket under the door, it gets clipped and the mathematicians get their train journey at a fraction of the cost the biologists paid.

The two groups run into each other again on the way home from the conference. This time the biologists are on to the game, so after exchanging a knowing wink with the mathematicians they send a representative off to get one ticket. But they are amazed to see the mathematicians don’t even bother with the single ticket that bought for the first journey. The biologists want to know what’s going on by the mathematicians stay tight lipped until their spy announces ’conductor on his way’. The biologist scramble just as they’d seen the mathematicians do on the last trip, squeezing into a bathroom. In contrast, all but one of the mathematicians strolls down to the other bathroom in the train while the other approaches the biologists’ room, knocks on the door and asks ’tickets please’.

(The moral of the story, biologists should think carefully before applying mathematical methods)

You have to be in to win… David Winter Feb 26

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Research Blogging Awards 2010 FinalistSo, in a fit of egotism and optimism I nominated myself (and a bunch of other people) for the Research Blogging Awards – putting myself forward in the category of “Best Lay-Level Blog”. The finalists were announced today and it seems I made the list. Apparently in the next stage researchblogging.org members vote for their favourite blogs in each catergory. I think it’s safe to say I’ll be out of the running once voting starts but I’m really quite chuffed and… damn it I’m just gonna say it… it’s an honour just to be nominated among real writers lie Brian Switek of Laelaps and Ed Yong of Not Exactly Rocket Science and the bloggers behind The Lay Scientist, Observations of a Nerd, Mauka to Makai and Cancer Research UK’s blog.

Congratulations to all the finalists but in particular to Aimee Whitcroft who does a lot of work behind the scenes at sciblogs and has been nominated in the chemistry physics and astronomy category.

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