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Posts Tagged ‘freezer love’

Year Six of Johns Freezer

Posted in Freezermas, tagged , , on July 7, 2018| 1 Comment »

I’m a few months late on the six-year anniversary of this blog but finally found some time. (For year 5 go here) It was seemed to be another quiet year on the blog because it was not a quiet year for work or other aspects of life. The DAWNDINOS project got into full swing and there will be a lot more about that soon on that website and maybe here, too.

Freeezersaurus 2 has been mostly vacated now; and Freezersaurus 3 is in place, with the contents shifted– and a mad rush in action to get rid of (boil down + varnish bones of) as many specimens as I can! I have way too many… of course, mostly elephant bits. Here are the last big bits left in Freezersaurus 2; we are intimidated to move them…

Stomach-Churning Rating: 3/10 until the opossum-digested-by-gator at the end, then 9/10, so hang tight!

Year 6 began with a post about a new paper! We published a big synthesis of data on what mammals turn their kneecaps into bone (or not), and how those states evolved. The story turned out pretty interesting and we are still pursuing some angles that it inspired, so stay tuned! Otherwise, the kneecap project (i.e. Leverhulme grant) has ended and staff/students have moved on (but published all their papers on it– well done, Sophie, Kyle and Viv!!), so it will fall quiet on that topic for a while.

Then we published another paper, and it happened to involve more sesamoid-y stuff! But with birds and their ankles, and some tantalizing evidence of soft tissue and organic biomolecular preservation. I’m still a bit amazed this paper happened and am pleased we got to collaborate on it.

Next, I got to ramble on a bit, about another serious topic related to science– this time, on blame.  I had forgotten about that post, and now on re-reading it it has fresh new relevance to me. All the more reason to keep blogging!

Smaller but better: Freezersaurus 3, part of a proud dynasty!

But then, what do you know, we published another kneecap paper! And on ostriches! With some simple but ambitious finite element analysis. We are meaning to get back to this approach… it just scratched the surface of some super cool “mechanobiology” that could shed light on “evo-devo”.

And next, BOOM! The dinosaurs dawned. By which I mean my current ERC grant “DAWNDINOS” began. Do take a look– the website now has some lovely NEW palaeo-art by Bob Nicholls, John Conway and Scott Hartman, with more to come! This project’s inception led to an inspection of caeca in tinamous; the following post.

I managed to have some summer holiday in the midst of the year, and that made an extremely memorable “pilgrimage” to a fossil site possible– “Experiencing the Irish Tetrapod Tracks” was the blog post that emerged from the waters. (That post needs a little revamp in light of some other literature; I will get around to that soon)

DAWNDINOS got a nice new 3D printer and we’re gradually printing up some archosaurs to show.

Holiday ended and back to the freezer I went, to post about how we thaw specimens (and how odd wallaby legs can be). Then we published three papers in quick succession and I played catchup posting about them (Mussaurus forelimbs; mouse vs. human hindlimb simulations; and tetrapod forelimb musculature).

Speaking of mouse hindlimb simulations, I didn’t blog about this related paper that we published earlier in 2018, but it’s very relevant. And GIF-worthy!

But I couldn’t stay away from bird legs for long, and so soon enough I posted “The Bird Knee Challenge“, which still stands.

Jumbo the elephant loomed into view at Christmas-time (plus a documentary about T. rex with Chris Packham, and another about Hannibal’s elephant excursion over the Alps– the latter also playing on PBS in USA); all featuring cameos with me, so I posted about the Jumbo/Attenborough one. That’s another life experience I will treasure.

Next, back to musing about science and humanity– and who’s a more big-name, very relatable human scientist than Darwin? Well, we could debate that endlessly but I posted about Darwin’s human nature for Darwin Day.

That takes me through to March 2017. I’ve posted a little more since then but that counts as Year 7 of this blog, so we’ll catch up with that then. Looking back on ~2017, I posted more blog posts than I thought I did! Maybe it’s just that 2018 feels very quiet to me blog-wise. We’ll see how it shapes up though.

Years ago, my team dissected an alligator (for Allen et al. 2010,2014 papers if you are keeping track) that had an opposum in its stomach, during winter when feeding wasn’t supposed to be happening much. So that came up again this year; and hopefully it does not make anything come up from your stomach. But this is real anatomy in action.

 

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You Thaw That, We Thaw These

Posted in Frozen Mammals, Mad Science, tagged , , , , , on November 23, 2017| Leave a Comment »

This week we conducted wallaby leg dissections for a study of the kneecaps of marsupials (pouched mammals). Placental (non-pouched) mammals like us almost all have bony kneecaps but many marsupials do not. Kneecaps do important things, acting like gears around the knee joints (e.g. this old post), and yet it is unclear why some marsupials have lost, kept or even re-evolved them as bones. So we’re investigating that and already noticed that one of our wallabies has bony kneecap(s) whereas the other doesn’t, so we’re checking out why and taking tissue samples to do histology (sectioning for microscopic imaging of tissue composition and structure) on so we can see what the knee tendon/kneecap tissues are made of. Some marsupials turn their kneecaps into fibrocartilage rather than bone or tendon and that can be impossible to identify without histology.

The wallabies are small, about 20lbs or so and just take a day or so. Like a turkey. And it’s Thanksgiving today, so here I am with a post about thawing specimens for science, rather than for food. Maybe the title will make sense now.

Stomach-Churning Rating: 7/10; thawed wallaby bits from the get-go.

Thawed lower leg and foot of wallaby. The stickers are for an old study that would take too long to explain…

This post was directly inspired by journalist Jason Bittel’s inquiry to me about my tweet on the wallaby thawing; he wondered if there might be a fun story linking thawing-for-science with thawing-for-Thanksgiving. Some highfalutin editors didn’t agree, so no printed/online story came of this, but I am not so highfalutin, hence this blog post.

Thawed wallaby forelimbs. I’m also looking into the “false thumbs” that some marsupials have (“sixth fingers”), much as elephants and other mammals may have.

Thawing is second nature for our lab’s team; we do it all the time. Avid readers will be unsurprised to learn that just about everything I’ve worked on has been frozen at some time, and thus has been thawed out at some time(s). Normally we don’t freeze if we need live tissue or undistorted tissue, e.g. to measure physiology or very fine microstructure– freezing disrupts all of that. We would instead use physiological saline solution or else a preservative like formalin. And you can only freeze and then thaw a specimen for two times or so before it becomes too useless even for anatomical study.

A small specimen like this salamander can be thawed out simply by running it under warm water for a little while or leaving it out for an hour.

We just leave specimens in a cart, or on a table or sometimes in a cold-room shelving area, for slower thawing. Space heaters tend to overdo things. We don’t do any rough calculation from some sort of thermodynamic first principles of time-to-thaw vs. specimen size (I wish we were that smart!); just seat-of-pants guessing and checking (yes, poking specimens to check their thawedness is a method of choice). Cutting things in half along the way, or skinning them, may be used to accelerate the thawing process. But it’s about as unscientific a method as we use.

The hardest specimens to thaw of course have been the largest specimens. Elephant legs can be >2 metres long and hundreds of kilograms (especially when frozen). A week at room temperature tends to work OK for getting them to a dissectable state. One has to balance the outer deterioration with the inner frigidness. We’re not so concerned about microbe growth in most cases, as one would be with a thawing turkey, and not at all about consumption. We just want to be able to dissect it and make observations, mostly via eyeballing the specimens as we dissect them,

Left hindfoot of an Asian elephant. Still frozen; this was bandthawed- I mean bandsawed- to see its internal anatomy nice and clearly. You may see this specimen again somewhere else– stay tuned! 🙂

Moisture and fluids can be a challenge: generally the rooms we thaw in are low humidity so moisture may not be an issue once the ice melts away, and we have drains nearby. We try to remove ice first or have towels to wipe/soak fluids up as thawing progresses. But if a specimen is sitting in a cart or storage bag with too much ice early on, that can thaw first and then turn the specimen into a nasty slurry of the stuff you’re interested in and the less desirable muck. So we try to avoid that.

De-thawing too early is bad. The smell gets progressively worse– and once the interior of the specimen is thawed enough, then bacteria get in there and the interior becomes a brewing ground for heat production (rather than remaining a cooler region), which accelerates decay, so we don’t want that. We have to check on thawing specimens regularly and move them to cooler storage areas, or begin dissection earlier, if the decay process is noticeably getting excessive.

Any insulation affects thawing time- so scales, feathers, thick skin, shells, fat (for a short while until it decays), and other layers will slow thawing—and may keep heat inside, if there begins to be thawing of the core. So sometimes you open up a specimen that seems dry and clean on the outside and the inside is unpleasant. But with experience that is not hard to avoid.

Thawed wallaby patella prepared for histology.

The foulest specimen I’ve thawed by far was a monitor lizard… it was shipped to me in California from Arizona when I was a PhD student. This was in August’s heat and the box of the big lizard sat thawing at the post office for 2 weeks before they contacted me and asked why a smelly box was bleeding. I came and got it and brought it back to our department but the smell was so bad it set off our building health & safety person’s alarm bells (sorry, David!) and they emailed around a “toxic alert” warning, until I bashfully made it clear that my lizard was the cause, not some toxic chemical. I got in some trouble and was very ashamed. But we put the specimen into a big tank of brine solution and the smell was reduced—the specimen may well still be preserved there 20 years later; I do wonder! Anyway, that experience was so horrendous – and I have a strong stomach—that I regularly recall it and seek to avoid a repeat. It was the most disgusting thing I’ve ever experienced. I do not recommend it.

What we tend to want to get from thawed specimens is: (1) descriptive anatomy (what connects where), and maybe (2) quantitative measurements (laborious metrics of “muscle architecture”– how much does each muscle weigh, how long is it, etc; over and over again for many muscles…). These data not only serve to tell us what makes animals different (and how this evolved) but also the data are used to test questions such as how animals work. In the case of things like wallabies, ultimately we’d love to know what their kneecaps do if they are bony or not; what difference does it make and why might there be differences? We’d spotted one wallaby already that seemed to have a bony kneecap on one leg, and a non-bony one on the other leg, so that asymmetry got us excited.

What’s surprising to learn about thawing animals for science? Well, my first thought is that it’s beautiful. I don’t tend to think of it as gross. I’ve rhapsodized about this before. Animals are wonderful inside and out, and I regularly pause during a dissection to marvel at how amazing the anatomical specializations of animals are. Simple details- shapes, colours, configurations- can be gorgeous. (Often the blood is minimal, drained out early, so that doesn’t detract from or hide the detailed imagery) The gentle yet complex path of a tendon around a joint can yield profound visual enchantment in its elegance. This is all the more true once one ponders how these complex structures evolved, and how much diversity of form and function is out there to study—and how little we know about it! We still don’t know well how to fix many problems humans have with their anatomy, and that’s orders of magnitude worst for most animals, because we don’t understand how anatomy works, or even what the anatomy is like in some cases. So that keeps me busy discovering things. Every specimen is different with surprising little variations, or big ones—sometimes there is one muscle, sometimes it is clearly divided into two muscles, in the same species or even the left vs. right legs. I love seeing those intricacies and wondering about them.

Thawed wallaby shank sliced open to show lovely digital flexors and gastrocnemius muscles. So many questions are raised by this!

If you’re thawing for Thanksgiving, or thawing for science, or thawing out family relations during a gathering, or thawing yourself out from the winter’s cold– my best wishes to you! May we all enjoy what we thaw.

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Full Freezer Five Thy Blogger Lies

Posted in Freezermas, tagged , , on March 3, 2017| 2 Comments »

‘Full fathom five thy father lies, of his bones are coral made. Those are pearls that were his eyes. Nothing of him that doth fade, but doth suffer a sea-change into something rich and strange.’

(Shakespeare’s The Tempest Act 1, Scene 2)

Stomach-Churning Rating: 1/10- this time, tame images.

Five years have passed on this blog now, and this year with them passed Freezersaurus (soon to leave RVC’s campus; sob!). Indeed, the blog has changed, via the tempests I’ve weathered in my own life, which I lamented in last year’s summary. Regardless, the blog has been visited this year more than in any prior year, with >101,000 visits– thanks!

This year I’ll keep my annual retrospective shorter than usual, as I’m feeling healthier and more energetic but less self-indulgent.

I still got to have fun, like this ComicCon in NOLA. So, some self-indulgence.

I still got to have fun, like this ComicCon in NOLA. So, some self-indulgence.

I began the past year by blogging about why I blog, and how I feel that in a way I (and others) have long been blogging even if it wasn’t called that, and how I don’t see science communication such as blogging or tweeting as something distinct from science itself. Reading back on that post, I find some themes there that emerge again and again throughout this year’s posts, such as valuing diversity (in its diverse forms) and curiosity.

Like this? So much more is here!

Like this you do? So much more here there is!

Never tired of elephant feet will I be!

Those introspective posts included one that is very close to my heart, about how I notice my own decline (some of it since reversed, but some still lingering) and feel grief. It wasn’t long after that post that I wrote more about my experience as an epileptic; what it’s like to have a seizure. Another, more science-focused (but still very human) one laid out my views on what my team’s principles are. Then I returned a few posts later with some reflection on how time passes (too quickly!) and with it come publications (I reviewed some of my team’s latest), among other changes as a person living as an academic. I wrote then that “I suspect I’ll look back on 2016 and see it as transformative, but it hasn’t been an easy year either, to say the least.” Yep. Spot on. I’ve started a big new grant which has been a huge challenge, and I’ve rediscovered my health and some of my old self with it, rekindling some passion and hope. Later, on USA’s Thanksgiving, I typed in some musings about my appreciation for diversity in the human world. Again, with thoughts of disturbing recent political/social trends weighing heavily on me, I celebrated how the Women’s March inspired me, and how that relates to the importance of curiosity and empathy.

He ain't goin' nowhere.

He ain’t goin’ nowhere.

But there was plenty of time here to talk about freezers and anatomy and research, too! We published a paper that I think I’ll long regard as one of our better ones, on using dynamic computer simulations to study how ostriches control their walking and running gaits with their muscles. Throughout 2016, we worked hard to get our anatomical research out there to the public in person. So I posted about our presentations at the Cheltenham Science Festival (including a public cheetah dissection, which was a huge hit!), and “Team Cat” did a dissection of another cheetah (all zoo mortalities) at the RVC for a well-attended joint event with UCL/Grant Museum on “Wild Cats Uncovered: movement evolves“. UCL’s PhD student (soon Dr.) Marcela Randau wrote a great guest post about our paper on how size and ecology relate to the shapes of backbones in cats, which tied in nicely with those big cat dissection presentations. I also ruminated about how scientists balance testing big questions vs. getting very accurate data, using the big question (in my and others’ research) about how much more slowly big animals can move relative to smaller ones as an example. As a final anatomical post this blog-year, I wrote about the biceps muscle, and people seemed to like that, so I will do more of those.

Whale humeral epiphysis (joint) turned into a sculpture with walrus ivory teeth, at Point Vicente Museum, LA.

Whale humeral epiphysis (joint) turned into a sculpture with walrus ivory teeth, at Point Vicente Museum, LA.

In addition to being open about my (and my team’s) thoughts, experiences, dissections and publications, we put a lot of effort this year into making our scientific and anatomical data public. My blog posts about our huuuuuge open datasets on crocodile and tuatara 3D scans exemplify a deluge of data that is going to keep coming out. We’re going to push very hard on this, including an effort to release old data from prior publications of mine. I’m thrilled that we can finally deliver on these things; it is a great feeling!

Yale Peabody Museum specimen YPM57100: ilium (hip bone) and vertebrae of the Triassic archosaur Poposaurus. More about this later!

Yale Peabody Museum specimen YPM57100: right ilium (hip bone) and vertebrae of the Triassic archosaur Poposaurus. More about this later!

We enter year 6 of this blog with a new (temporary, maybe) freezer, which we failed to reach a conclusion on naming. I’m sure you’re on tenterhooks awaiting the final decision. I have a bunch of ideas for some blog posts to come soon (really fun anatomical papers en route), and I always welcome guest posts so let me know if you want to do one! In the meantime, I sprinkled some images from my 2016-7 travels here in this post. With good health comes more ability to go do fun things that I’ve put off while recovering, so hopefully 2017-8 will provide some new images to share.

A sunny Sceloporus fence lizard seen in LA.

A sunny Sceloporus fence lizard seen in LA. Meanwhile, the UK awaits some sunshine…

I doth not protest too much, methinks– there have been some good times this past year, and ides of March be damned, I look forward to sharing more science here for year 6!

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Goodbye Freezersaurus, Hello Freezy McFreezerface?

Posted in Utter Frivolity, tagged , on December 13, 2016| 4 Comments »

As attentive readers may know, Freezersaurus died over a month ago. We’ve been thankful for the winter’s chill that slowed the thawing process of our treasure trove of specimens while we complete the move to a temporary freezer. The gelid torch was thus being passed to the next walk-in freezer at a glacial pace– but with the glacier-scale force of Team Hutch’s collective muscles.

Stomach-Churning Rating: Hmm tough call; 6/10 if you know what it’s like to clean out a nasty freezer, 4/10 if not.

Aww. The freezer-moving team is not thrilled by the task ahead.

Aww. The freezer-moving team is not thrilled by the task ahead, and is exerting their frowning-muscles. (photo: Sophie Regnault)

Santa (Jim Usherwoodclaus) brings a bag-- of elephant feet!

Santa (Jim Usherwoodclaus) brings a bag– of elephant feet! (photo: Sophie Regnault)

Yet this week it all ends. With Crimbo’s long break ahead and an uncouth urinal smell pervading the dripping carcass of Freezersaurus, we have to clear out our little frozen ark. Some specimens have had to meet the incinerator early; others have returned to frozen limbo pending our future attention; and some are now just clean bones.

One of our many young emus that needed cleaning after thawing; here, just the right leg bones.

One of our many young emus that needed cleaning after thawing; here, just the left leg bones.

Quite a puzzle: one young emu's skeleton to reassemble in the future. Thanks to Sandy Kawano et al. for cleaning help!

Quite a puzzle: one young emu’s skeleton to reassemble in the future. Thanks to Sandy Kawano et al. for cleaning help!

Horse forelimb from an old joint range-of-motion study we did; now reduced to bones (why did I keep this frozen anyway? who knows).

Horse forelimb from an old joint range-of-motion study we did; now reduced to bones (why did I keep this frozen anyway? who knows).

So our temporary new freezer could use a name; Freezersaurus II just won’t do. In the spirit of democracy (and Yuletide), I’ll open the floor to nominations. Nothing could go wrong with populism, right 2016? Hello? Oh crap.

Last cartful of elephant feet!

Last cartful of elephant feet! (also: keen eyes may spot some gory graffiti)

Last look at Freezersaurus: Inside looking out.

Last look at Freezersaurus: Inside looking out.

Last look at Freezersaurus: outside looking in. Ice still lingering on the cow and horse legs from old XROMM studies.

Last look at Freezersaurus: outside looking in. Ice still lingering on the cow and horse legs from old XROMM studies, at the back, past the slurry of blood.

Enjoy some photos of the move, and please make freezer name suggestions in the Comments.

Our new digs, for the time being.

Our new digs, for the time being.

And, if I don’t post again in time, Happy Holidays! May the dark times not Krampus your style.

-John, Dean of the Demochilling Polarpublic of Freezevania

Let’s let Mike Ness sing us out…

UPDATE:

OK we have, via various forms of social media, these nominations for our temporary freezer’s name (I took one from each person suggesting a name;  I hope I caught them all); so let’s open it to a poll!

link:

[Wordpress is not showing the poll on all browsers so you may have to click the link]

(The nominations: Freezersuchus, Freezertherius, Freezopolis, Eofrigidum, Narnia and Pleistoscene)

While you’re at it, check out Anatomy To You’s new blog post: do turtles wiggle their hips and if so how much? Now we know!

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Thanksversity

Posted in RANT, tagged , on November 24, 2016| 9 Comments »

First, a moment of silence for Freezersaurus (2009-2016); Rest In Recycling. This week we close the door on our years of arctic antics together. A new, uncertain relationship is beginning, with our diversity of icy inhabitants hanging in the balance. A future post will provide an update.freezer

Stomach-Churning Rating: 2/10; no photos, but some politics; take it or leave it.

Speaking of diversity, it’s Thanksgiving in my home of the USA and thus a time for reflection. Such reflections this year inevitably turn to current global events, in which “diversity” has come up in many ways, and then back to my own life, and back again. It certainly has been a year for reflection, and – like many others – my current taste for dystopian tales mirrors that reflection.

In (the United States of) America, Thanksgiving is a tradition of (at least implicitly) commemorating the meeting of two cultures (Native and newly-immigrated American/Puritan) and the eventual fusion/phagocytosis of those two diverse cultures into something new; leading to the USA of today and its diverse inhabitants and cultures. We spend time with family and have awkward conversations or cheer on sports teams or take engorgement-induced naps. We eat diverse foods of the harvest time and thank the spirits/divinity/cooks for their bounty. Many Americans, across our cultural diversity, take time to ponder what they are grateful for. I’ve always loved this holiday because of that, and my fond memories of past Thanksgivings.

And so I am drawn to reflection on the giving of thanks, and the significance of diversity, and I choose today to type some words that echo my thoughts.

I am grateful for what diversity we have. My life is enmeshed with that diversity: I study biodiversity and marvel at the diversity of nature, which both bring great joy to my life. I worry about the state of funding for, and reciprocally the appreciation of, the scientific study of nature and the human value placed on biodiversity, and the implications of those for the future of diverse life on Earth, both human and non-human. It is well known that they are all under threat, in diverse ways, from sociopolitical and other factors.

To me, human diversity (cultural, ethnic, other) is part of this natural diversity; it has evolved and will continue to, for as long as it exists. It is not going away. I am grateful for that human diversity. Some parts of it bring me terrible revulsion, and those are the source of much worry, and our own nature is their source, too. But it brings my life great meaning to interact with different people, to learn new things from them, and to share experiences in more positive ways. I am curious about all of these things, and because of that curiosity in 2016 I have learned more about that human diversity than I ever have before. Some of that learning has been about the dark side of humanity, from political and social trends (or glaring exposure of longstanding biases) in the UK and USA and more globally. Yet also some of that learning has been about the virtues of human diversity and realizing how much solidarity I feel (and have long felt) for those who are trapped in disadvantageous positions along the fault lines of confrontations between different components of that diversity. It has brought out some of my best and worst feelings.

Like a snail, this year I feel that I have periodically been moving forward to inspect the greater world, enjoying it for a time, then recoiling once I encounter the xenophobia, anti-intellectualism, and selfishness, which make me want to stay inside my shell. Long have I inhabited that shell in 2016. I’m not proud of those feelings and that tenancy in my little partition of this world, but they are what I’ve been able to manage. Today, I am trying to appreciate the broader picture and remind myself of where there is still goodness in the world, and how cycles of diversity can stabilize. We have choices to make about how we control those cycles; we humans are unique in our control of them; and those choices are best poised on the understanding that comes from curiosity. It is there in that diversity that Darwin celebrated; “There is grandeur in this view of life,” and today I am thankful for the grandeur that does still remain around us. I am curious to view what grandeur that diversity presents next. We could all use more of that grandeur.

And thanks for reading this post.

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Frosty Fourth Blogoversary

Posted in Read Me First, tagged , on March 2, 2016| 2 Comments »

Anatomy of an amoeba: why not? I like it.

Anatomy of an amoeba: why not? I like it.

Well I made it this far, and I might not have expected to last four years of blogging but I did last, and I’m very glad. Here is my customary retrospective with some “new” images. I’m glad to see that you’re still here, too: over 3200 blog subscribers (roughly doubled since 2014?) and some regular commenters remain– thank you! Like an undead horror, this blog keeps lurching forward, and it appreciates loyalty.

rick-what-sm

 Stomach-Churning Rating: 5/10- there’s a bit of blood and stuff. Nothing that unusual. If you’re like Rick (above; by /u/epicolllie), that won’t phase you by now.

The past year on the #JohnsFreezer blog felt quiet to me, and that’s largely because I was distracted by numerous things; if you know me (or follow my whining on Twitter), you probably can guess. But there were enough highlights to keep me feeling satisfied. Judging from your reactions, you liked my inside scoop on the T. rex Autopsy documentary that I consulted on, and a distant second place post was, hmm, that’s kinda surprising: my elephant foot dissection post. I’m rather pleased so many of you clicked on that one, actually. That’s a meat-and-potatoes post for this blog, much like my latest one on getting to know M. caudofemoralis (longus). But hey, check out the “Goat to be Seen” post if those are your kind of entries– it seems a lot of people missed that one, and it had a mix of quirkiness, unflinching raw anatomy, and art that still makes me smile.

I was browsing my photos and ran across this NHMUK exhibit of a small ungulate hooved limb vs. a nice honking big padded elephant foot. It elegantly gets across the biomechanical differences between these limb structures.

I was browsing my photos and ran across this NHMUK exhibit of a small ungulate hooved limb vs. a nice honking big padded elephant foot (both abstracted down to their fundamentals). It elegantly gets across the biomechanical differences between these limb structures. Bravo!

My rants about how sometimes it’s helpful for scientists to put the brakes on media coverage of their own research, and on “HONCOs” (honorary co-authors), also brought in the punters, as did the re-post about the not-so-bad aspects of self-promotion in science. Not so many people appeared to read the post about where ideas come from in science but it got a lot of tweets, which is a strange incongruity, yet my thoughts on how to manage a research team didn’t do any better (but if you read in between the lines, there’s a poignancy to that post). Anyway: good ole rants; ahh, it still feels good to have those off my chest, even after all these months. And writing them helps me sort out my own thoughts, if nothing else.

Hindlimb of a sea turtle that we dissected in 2015 after it came in for a clinical postmortem.

Hindlimb of a sea turtle that we dissected in 2015 after it came in for a clinical postmortem.

One of my greatest science heroes, “Neill” Alexander, got his due here, and there continue to be comments trickling in on that post from people who are reminiscing about his influence on their careers. That is definitely one of the posts on this blog that I feel best about, even after four years. It meant a lot to me, much as Neill has meant a lot to others. I also did an homage to museums, which in parallel (oddly, but enjoyably for me) became an(other) homage to avian kneecaps. I like them too, and museums of course, but they’re awesome in a very different way from Neill.

Team Cat is still cranking on our biomechanical and anatomical studies of felids- expect a lot of new stuff from us in 2016! Meanwhile, enjoy this spectacular taxidermy.

Team Cat is still cranking on our biomechanical and anatomical studies of felids- expect a lot of new stuff from us in 2016! Meanwhile, enjoy this spectacular taxidermy– and check out Dr. Andrew Cuff’s blog with the latest science and stories.

I learned a lot about my genome in this fourth year of blogging, and I delved into that with you, as part of my commitment to share what I learn about myself by poking around in my biology. Oh, and I just learned that the image depicting my genomic ancestry was this blog’s most-clicked image this year– that’s cool, and unexpected!

The past year was a big year for dinosaurs on this blog, with a post on the “Giant Dinosaurs of London” and another related to my cameo in the giant titanosaur documentary with Attenborough, but with a focus on dissecting dinosaurs, and a blatant bandwagon tribute to/musing on Jurassic World.

The very, very strange iguanodontian dinosaur Lurdusaurus (forelimb; note the big spiky thumb claw), which I was pleased to see at the natural history museum in Brussels, Belgium in 2015.

The very, very strange iguanodontian dinosaur Lurdusaurus (forelimb; note the big spiky thumb claw), which I was pleased to see at the natural history museum in Brussels, Belgium in 2015.

And finally, this blog had a baby, or a sister, or whatever, this year, and that has been a blast: Anatomy to You was born, thanks to Dr. Lauren Sumner-Rooney’s expert care and dedication to science communication. If you haven’t checked it out, now’s a good time, or offer to do a guest post for our “In Focus” section if you’ve got some anatomical science to share! Speaking of guest posts, Julia Molnar did a fabulous one about our paper on crocodile backbones this year, here on this blog.

I'm still cleaning up specimens from the freezers: here, some "emu butts" (tails) from a collaboration with Michael Pittman and Heinrich Mallison, and PhD student Luis Lama's past thesis work.

I’m still cleaning up specimens from the freezers: here, some “emu butts” (tails) from a collaboration with Michael Pittman and Heinrich Mallison, and PhD student Luis Lama’s past work. Something about these vertebrae fascinates me.

I didn’t deliver on some plans for this year, such as a komodo dragon anatomy post, but I did finally do the “better know a muscle” and “dissecting dinosaurs” posts I planned, and a few other things, so the year worked out well enough.

What’s coming in year 5 of this blog? I have no bloody idea; I have not gotten that far. I think we’ll all be surprised. Let’s make the most of it! (I will consider requests)

"We'll always have elaborate models of gorilla muscular anatomy in Paris."

“We’ll always have elaborate models of gorilla muscular anatomy in Paris.”

 

 

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A Third Year in the Freezers

Posted in Read Me First, tagged , on March 3, 2015| 6 Comments »

Claws for alarm

Claws for alarm

Happy Third Blogoversary, WIJF blog! I am thick in some paper-writing, so I can’t write my usual detailed summary of the past year. Or so I thought, then I started writing and finished it, so here it is! I didn’t feel I needed to post this, but I like retrospectives and writing this helps me recall what happened here and gives me new ideas for the future (or things to avoid!). I continue to enjoy blogging here and you’re still here too, so that’s enough for me, regardless.

 Stomach-Churning Rating: 8/10; some unpleasantness in the images ahead…

Indeed, this year saw an odd leap in blog subscribers, from about 200ish to now >1500 since around August 2014; an astonishing sevenfold increase in about as many months! I did not see that coming. I’d love it if some of the new folks could speak up in the Comments and say what brought them here (this WordPress recommendations link? BBC Dinosaur story link?). Otherwise, Twitter won the social media “war” again against Facebook for bringing people here.

The top post of this past year was easily, and unsurprisingly, the evil takeover of the blog by my Sith nemesis. May she remain in her galaxy far, far away and not trouble us again. “Aren’t Adaptations Special?” (my ode to the 35th Spandrelversary) and “Co-Rex-Ions” (my chronicle of correcting a paper and reflecting on that experience) both did nicely, too, in terms of readers.

Insanity claws

Insanity claws

The latter post had parallel threads with others exploring my career and my role as a research manager/mentor, and pondering (with your input) research data “versus” conclusions as well as an awkward day earlier in my career involving crocodiles and karaoke. A recurrent theme that you may have noticed is that I am using the blog to explore my tolerance for humiliating myself (or at least self-effacement), and exploring why we humiliate others, which still fascinates me.

It was also a deeply introspective year for me, for reasons made clear by this post, which links to other posts like it exploring my experiences jousting with mortality and its reverberations. It has been an… eventful year. Leading to many thoughts bouncing around my head like happy little blood clots.

And then my crossover Conversation UK article was posted in full length here, “Anatomy: Dynamic, Not Defunct“, which was for me a highlight of the year on this blog (and my sci-comm efforts). I followed up on this big-picture anatomy motif in related posts on “In the Name of Morphology” and an ode (it was a year of many odes!) to anatomist Richard Owen.

My two-post stroll through the British Museum also got me writing about how animal anatomy plays a physical or at least visual role in human art and culture; that was fun for me. Likewise, I did another anatomically-focused museum exhibit review for the NHM’s mammoth exhibit, and yet another on my visit to another “home of anatomy” in Jena, Germany‘s equivalent of the NHM. That post’s ontogeny-phylogeny theme, echoed in my Owen post, also tied into a long-form version of a Nature News & Views article I wrote but also posted here, on “plastic fishapods.” Expect more evo-devo from me in the future; it has become part of my research programme to tie together form, function, development and evolution in my team’s work.

Ontogeny havoc

Ontogeny havoc: teratologies

In other, more random anatomy-based posts, there was an early one on cat dissections, another on the lives and deaths of penguins (there will be more on this topic soon!), and the most recent post on mammalian tails. Finally in 2014, as one of the highlights of my career lately, we published 3 papers about bird legs/knees on one day, in the open access journal PeerJ, right before Crimbo. I’m proud of the work my team put into those papers. 2015 looks to be at least as productive and fun!

This blog still has legs!

This blog still has legs!

Keep wearing layers of clothing. I’ve got plenty more freezerness in store on this blog; freezerburnout has been avoided. Expect posts on dissecting dinosaurs, that promised komodo dragon post, more cats and penguins and then definitely more bird (and lizard, and mammal!) knees, and something special about genomes. I also have some changes in mind for the blog, with a new flavour of regular, short posts. I’ll save the explanation for later.

What are your memories of the past year in my freezers?

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What’s In John’s Freezer… For You?

Posted in Guestsicle, tagged , , , on January 20, 2015| 13 Comments »

Stomach-Churning Rating: 1/10 for ambiguous sacks.

I mainly post here about my team’s research and interests, but today I felt like sharing something special and concrete: the contents of our freezers. They are not just John’s and there’s more than one freezer; thus there is room to share, within reason. So if you’re a researcher, especially in the UK/EU, needing unusual research specimens/tissue, you might want to contact me to use them. This blog’s posts summarize most of what I have available, and for security/other reasons I don’t want to get into deep detail here, but we sport a respectable collection of limbs/bodies of animals like:

Birds: ostriches, emus, broiler chickens, guineafowl, assortment of others.

Crocodiles: Nile, Osteolaemus, Morelet’s and some others (1 Melanosuchus, 1 normal Caiman).

Squamates: a monitor lizard or two and some other random lizards.

Amphibians: a few fire salamanders and such.

Mammals: of course, plenty of elephant bits (no ivory!), rhinos too (no horns!), giraffes, a dwarf forest buffalo, alpacas, deer, pieces of camels and zebras (feet etc.), wild cat species (no penises!) and a few other things. And then the usual assortment of veterinary species like cows and horses. A heavy focus on limb material– very few if any heads, torsos, etc.

This is in addition to a nice little comparative skeletal collection, focused on cleaned members of the above groups and a smattering of others. Nothing on the scale of RVC’s marvellous Anatomy Museum, but we’re young.

And two African land snail shells (inhabited) I was reminded of during a recent inventory… Here are some of my helpful helpers in that inventory extravaganza!

inventory

Especially if you’re searching for CT scan data (sooner or later these data will appear online; I want it to happen!), tissue samples for genetics or cell biology (if frozen is OK!), comparative anatomical specimens to inspect, or other uses of frozen anatomy (photography? other art? We’ve helped artists before!), the freezers might be able to help you! The less destructive, the better, but even some destructive analysis might be OK. We regularly accommodate visitors, either independent ones or collaborators, and I aim to provide good hospitality when I can accommodate them!

Get in touch with me if the above description is you. It’s not an open invitation to everyone, but for valid research purposes I can and should try to help. But I’m limited by time and other human factors, so I can’t do everything and help everyone. Our ability to host others to come work on our specimens here in-house is very limited, I’m sorry to say. The primary purpose of all the hard work we’ve done accumulating these specimens remains to support our research, but there’s room to help others too, and we want to maximize the impact of our research collection, including potentially on teaching and public engagement with science where feasible. So I’ve put it out there, and that ends this post.

UPDATE May 2016:

I am planning more freezer cleaning; under more pressure due to dwindling space; so if specimens here interest you and you’re EU-based, I am possibly up for loaning out material. Conditions: (1) you do all transport pickup and return; (2) skeletal material is kept intact unless I approve in advance; (3) 2 year-ish loan at most, informal. We are curating material, so it must return– and it must stay in the EU (ideally UK) if on loan. Everything gets CT-scanned before it goes out. Not everything is up for grabs, but there is room for negotiation as to what’s available or not. For scientific usage only! Best to email me if interested.

Is there something in the "Non-Elephant Freezer" for you?

Is there something in the “Non-Elephant Freezer” for you?

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Just-So Science: revisiting Kipling’s kangaroos and elephants

Posted in Frozen Mammals, tagged , , , , , , , on June 26, 2014| 1 Comment »

A very short post here to plug BBC Radio 4’s excellent second series of “Just So Science”. These are 15 minute stories involving a reading of parts of Rudyard Kipling’s great British/natural history stories, and then examining how the science of today informs us about the real lives of animals, without resorting to just-so stories a la Kipling (co-opted as a term in evolutionary biology, too!). I was featured last year on rhinos.

I’m featured this year on kangaroos (now available online) and elephants (also available online now). I just listened to the kangaroo episode and it was good fun. I’ve studied the biomechanics of kangaroos a bit, in as-yet unpublished work featured here in a BBC News story (video from that work is below), and we’ve done other work on their bone morphology and how it relates to body size that is sure to come out in not too long.

Don’t blink! Or, for your enjoyment, a looping GIF:

kangaroo hop

My freezers feature heavily in one bit, in which you can hear me vent my frustrations about an unlabelled bag and stacks of specimens– where is the wallaby? And what’s that crinkling noise?

Best beloved, it is the sound of science. Just so. Enjoy!

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What’s in Year 2 of What’s in John’s Freezer?

Posted in Read Me First, Utter Frivolity, tagged , , , on March 3, 2014| 11 Comments »

Hey I almost forgot, it’s the blog’s second anniversary! What the hell happened this year?

Stomach-Churning Rating: there’s an 8/10 photo of ostrich guts here; otherwise 2/10ish.

I bring you tidings from the past and future!

I bring you tidings from the past and future!

This was the Year of the Rant, and I enjoyed ranting to you on this blog. Sometimes you ranted with me, and that was even better. It kicked off with that cat documentary that spurned me in a feline dismissive fashion, then I lit off on documentaries in general and how they should give more back to scientists (what a discussion in the comments!!!!). Ooooh that felt good. And helped me sort out my thoughts about the topic. And after then, I got paid more often and still did a lot of documentaries– if you haven’t been watching Secrets of Bones on BBC4, you should be weeping bitter, bitter dregs (and be scrambling to get access). Catch me tomorrow (Tues) night with some of our emus! They paid me reasonably and in return I worked hard for them; before, during, and after filming, and I think we all felt good about it. Or I did anyway. The show is excellent, so I feel even better!

Sneak peek from BBC4's Secrets of Bones episode 3... recognize anyone?

Sneak peek from BBC4’s Secrets of Bones episode 3… recognize anyone? (from their website)

But no ranting palaeo-related blog would be complete without a good T. rex rant, and I did that this year. Took a big dump on the scavenger-predator non-troversy. That went over so well, Slate picked it up– I never had expected that to happen! I also appreciated how many colleagues joined in to condemn the senseless perpetuation of this dead issue by the media and a few scientists.

There were also some posts on more introspective things, like the feeling of being lost that pervades both visiting a strange foreign city and doing science. And like how science needs both the qualities of a Mr Spock and a Captain Kirk. Those were fun experiments in combining  a personal, internal experience with a broader message.

Darwin greets Chinese visitor Microraptor in my office.

Darwin greets Chinese visitor Microraptor in my office.

When I asked for suggestions last year, you wanted more coverage of other people’s stuff, and so I did that to a degree, reviewing the All Yesterdays and Unfeathered Bird books. And then I fell off that wagon, which I may come back to. But along the way I realized I don’t enjoy writing about papers that other people have already published because, generally, I then lack the personal experience of doing the science and showing it in progress, which is what this blog tends to be about and what excites me on a personal, visceral level. Once the paper is out, I feel like the cat is out of the bag and it’s not as fun to talk about unless it’s totally mind-blowingly (A) cool or (B) idiotic. Anyway, I might do a solicited post if someone gets me excited about a paper before it comes out, or who knows, I may change my mind.

Entirely unfeathered Indian peafowl in matching views.

Entirely unfeathered Indian peafowl in matching views, with Unfeathered Bird’s author-illustrator.

I also posted on a fabulous blog that more people need to hit, because you may be surprised just how fascinating it is- Veterinary Forensics. I get the feeling often, both on my blog and from scientific colleagues, that veterinary anatomy/pathology issues are seen as “lesser science” than basic, even descriptive anatomy. Somehow, insanely weird diseases or pathologies don’t excite people as much as insanely weird “normal” anatomies. I know there are exceptions to that generalization, but I think it’s a common (mis)perception people have, and part of it is likely because those fields (veterinary medicine and zoology, for example) are historically separate, and people tend to see anatomy and pathology as separate things- as opposed to points along a continuum. Since coming to the RVC, I have come from that kind of a misperception to one in which pathology enormously enriches my understanding of form, function and evolution. I also love the “applications of basic science to helping animals live better lives” angle. We should all be trying to do that as scientists, but from time to time I notice that it isn’t taken seriously (I even get reviewers’ comments bluntly stating that it’s none of our business as basic scientists, or for anatomy/experimental biology journals to mention!). Whoops better stop there or I’ll be writing a new ranty post!

Can't get enough of this -xray GIF, so here it is again.

Can’t get enough of this x-ray GIF, so here it is again.

Darwin Day got into some of the vet-y issues regarding feet, in a post on hooves and then another on pigs’ feet.

Toward the end of the year I got some guest posts going, by two main people from my team: Sophie Regnault on rhino feet, and Julia Molnar on crocodile spines. I liked those posts a lot, and so did you, it seems, so there will be more of those coming in year 3. Quite a few are planned already.

One of my favourite papers I’ve ever done came out this year, by Vivian Allen et al. on dinosaur body shape/postural evolution, and that went nicely as a blog post with tons of extra context and stuff. Digital 3D dinos, what’s not to love?

I was on sabbatical for much of the year, so I was posting a lot about patellae (kneecaps) and how fun they are to study, which led to posts about basal bird skeletons and more, like Darwin’s chickens and a joke about cake that only I seemed to find funny, and ending with a grand summary of avian kneecaps. I also reported on some new (post-sabbatical) research, still ongoing, with Dr. Stephanie Pierce and Dr. Maedeh Borhani at the RVC, on how salamanders walk. During Freezermas, I plugged our new comparative cat project.

The mesenteries are so gorgeous!!!!!!

The mesenteries are so gorgeous!!!!!!

Speaking of Freezermas: It happened, it was terrifying, and we’ve all grown from the experience of surviving it. I had a blast dissecting that ostrich, and the x-ray pics were a hit with everyone, too!

Then there was random “freezer love” and assorted posts to give insight into the daily life of a freezer manager, such as doing an inventory and reflections on childhood. I snuck in a tour of Dublin museums and the amazing Crocodiles of the World near Oxford. I meant to do more of those “anatomy road trip posts” and still aim to.

And we ended the year by ending the ongoing drama of the Mystery Anatomy competition, starting off a new year with a new scoreboard. We got more poetic and lyrical in 2013 with the answers to those mysteries, and that will continue (groans from those who are poetically challenged).

Elephant skull mystery x-ray

Elephant skull mystery x-ray

Some brief numbers: view-wise the blog has been pretty close to last year; about 87,000 views in the past 12 months for a total of almost 200,000, wow! This year, Twitter just barely edged out Facebook for bringing people to the blog (3,134 vs 3,022 clicks) but then geenstijl.nl bizarrely brought 2,732! There was no big Reddit or other social media site moment this year, but various sites and links continued to bring in a steady flow of visitors to add to the Google-search-firehose’s. Thanks to folks who linked here!!!

What google searches brought people here the most often? The top 3 are the most interesting; the fifth one just makes me laugh because I’ve never discussed Deepstaria enigmatica anatomy here, but will continue to promote people finding the site by searching for it, if only to annoy cnidariologists:

rhino 83
giraffe 76
camel anatomy 62
what’s in john’s freezer 60
deepstaria enigmatica 56

I’m a little surprised “elephant” and “dinosaur” don’t bring as many searches here, but there are probably more sites about those animals and hence I get fewer of the hits. Looking forward to more hits on “ostrich anatomy”…

My two top rants were the top posts this year, and that’s no surprise given the comments and other attention they got. Thanks for helping by participating! Those were nice group-rants. Healthy and vigorous. Shockingly, a poetry round of mystery anatomy came in 3rd! People just liked the chickens + bones + poetry. Those, and some hits from year 1, broke the 1000-views marks.

Americans came here in a 3:1 ratio to Brits, which means that Brits punched above their weight per capita (~5:1 ratio)! Canadians, you tried, too. Here, have some back bacon of dubious provenance. 🙂 Saint Kitts and Nevis with 670 views, wow! Very unexpected- you beat Italy and many others!

Most importantly, the blog has been about sharing my passion for anatomy (as preserved via freezers). I shared a conference talk about this subject here, using the blog as a prime example, to a warm reception. I want to try experimenting in new ways to use the blog to share things this year. I think you will like what I (we!) have lined up. Thanks for showing up and staying with me!

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