Beam me up, Squiddy

Science is important. It doesn’t fall to someone like me to explain why this is the case, but it’s as plain as the nose on my face. Virtually every aspect of human life these days is the result of science,  mathematics or engineering. Just think about it and you’ll see what I mean. 

Science got us past the edge of the map.

Now, I don’t know about you, but it seems to me that science and, well, reason have taken a bit of a smackdown in recent decades. Notions like Intelligent Design, flat earth and all manner of pseudoscience stubbornly refuse to let go. Don’t ask me why. I believe it was Plato who once declared that everything becomes it’s opposite. 

Anyway. 

The flipside of this groundswell of anti-reason threatening to sink us like a stone is that the average person (of a non science bent I mean) is not willing or able to bother making sense of science when they’re presented with it.

I personally encountered some alarmingly bad science communication along these lines last week.

Are you sitting down? Good.

I was at a marine sanctuary, enjoying the jellyfish and other beasties and trying to blow my camera up from overuse. At the same time I was overhearing one of the tour guides telling a group of visitors that cephalopods are aliens. 

Take me to your leader.

….Aliens.

No, not the illegal kind crossing the Rio Grande looking for minimum wage jobs in the US of A.

The tour guide continued, stating that ancient comets brought alien bacteria, which infected the earth. He didn’t really connect the dots too well to explain how alien bacterial DNA translates into extraterrestrial cuttlefish.

First off, a cephalopod is an octopus, squid, cuttlefish or nautilus. Creatures of that ilk. 

Ok, that’s my scientific contribution to this blog post. Now I will outline my thoughts on this miscarriage of scientific communication. 

The tour guide made a very common mistake. He took an outrageously twisted headline and ran with it, proclaiming it as gospel truth. This is happening an awful lot these days. In this new age of social media, shameless manipulation of research findings into public friendly pap and clickbait, thinking rationally about media is a dying art form. 

A quick run through Google turned up a bunch of headlines on this very topic:

Let the fun begin!

None of these headlines suffice to say came from publications remotely interested in objective science media and reporting, but from the other end of town. 

Reading through some of these headlines made me even more cross! I take this stuff seriously. When journalists and media outlets abandon integrity at all costs and essentially make stuff up I get pissed off. It’s like going to a restaurant and ordering kangaroo with a cranberry jous to to find the jous is packet gravy and the kangaroo was peeled from the underside of a semi trailer last week. In other words it’s crap. In this situation I’d ask for my money back (or my wife would).

If only we could get compensated for shoddy journalism like this!

What’s dangerous about this regurgitation of flawed information is that Joe Public doesn’t know the truth and doesn’t really think to question it. So as a result several dozen people are now out in the world believing that octopuses come from outer space.

The tour guide should be fired. With a baseball bat.

According to some of these articles researchers have concluded that the octopus genome is utterly unrelated to all other life on earth and their DNA originated in outer space.

Both points are utter crap. First, octopuses are related to every living thing on earth- including you and me. We all share a common ancestor. Not much seperates humans; who have obtained such lofty heights from bacteria. About 10 percent of my DNA differs from that in bacteria. I guess the octopus falls somewhere in between. Second, in no way shape or form has anything as complex as DNA been found in space. The only DNA in space as I write this post is astronaut DNA (and hitchhiking bacteria-from earth!!)

EVERYTHING on earth is related.

Bad reporting of science can only serve to harm society in the long run. I think just as important as reporting science is reporting shonky dissemination of it. Those of us who are passionate about science (it’s a search for truth after all, right?) need to pay attention to this. It damages science. 

We can’t have damaged science. 

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Harder than it looks.

Ok. So, as a handful of people on this planet know, I make Youtube videos. They’re not widely subscribed to yet, (or ever?) but I keep on making them because they’re fun and interesting. Plus I need to remain involved with science somehow, instead of watching my degree moulder away on a wall. 

No, future in science, come back!!

I am learning a lot about the process of video production. There’s a lot to it; more than simply whipping out a handycam and filming something. 

I will attempt in this post to go through the basics of making short youtube videos, and various aspects of the whole business that make themselves apparent along the way. Here goes…

How a Ben’s Lab video happens

When I began my channel about six months ago I had no equipment,  save for my smartphone. That was it. No microphones, no ridgey didge software (except an app on said phone), no tripods, no nothing. Nada. Zip. Zilch. I did have the desire to do it however,  and that is far more important.

So true. Will propels us. A car is only as good as the foot on the accelerator pedal.

So, armed with said phone,  and with no idea what I was doing I jumped into my first video;  a little introduction to strange marine creatures called phronima. 

I remember the making of that video being a series of engineering issues: for example I had no tripod, so I made one from milk crates and a chunk of styrofoam. Hell, it did the job. You have to be MacGuyver sometimes.

That video taught me a few things from the get go. 

What’s my line?

Writing at least an outline of what you’re going to talk about is kind of essential. I am not one of these people who can get up in front of a crowd and roll out some beautifully crafted speech. I mumble and I speak too fast. I know this about myself. Getting flustered and tripping over my words is very easy for me to do. So, if you can’t stare lovingly into the camera like you’re making love to it while you rattle off fun facts…..read from a script. By this I don’t mean read robotically like a ten year old at a school assembly.  I mean have a written script handy (in your hand if need be) and refer to it periodically.

Referring to notes won’t detract from your presentation, despite what you might think.

Having notes will nudge your confidence just that tiny little bit, and that is all important. Just don’t spend the whole video checking them. This leads to another discovery.

It’s ok to ask for help. 

With one or two of my early videos (hell even now I think my delivery is lacking) I found that I absolutely suck at talking to a camera. It’s surprisingly tricky to do. That bloody thing just stares at you, and I always have the feeling that it’s an unimpressed stare. I think that if a camera was an animal it would be a cat.

I’ll let you know when I need you.

Yes, it’s a hell of a thing the little enemies we face every day. Ok, so I’m no public speaker,  but I’m not going to let some gadget shoot me down. I’ve got videos to make. What I discovered helped an awful lot was having someone else present. In this case my beautiful supportive wife:

KAPOW!!!

I tend to mess around when I’m with people. Taking life seriously is something I try to avoid. It’s already serious enough. It doesn’t need my help. So, I found that when she’s behind the camera I relax a little. Or a lot. I could feel the difference in my demeanor when she was around. I’m not a baby. She doesn’t cut the crusts off my bread or anything, but she helps. A friend or even a pet can help you relax. 

These nebulous aspects of video making are big issues to address. In upcoming posts I’ll talk about other things I’m learning as I go…

Non-human microbiomes

This post drew on elements of my own Honours project, which I undertook in 2008. Yes, it’s been awhile, but I still love science. I hope this is interesting to someone. Please feel free to comment.

Microbiomes seem to be the talk of the town at the moment. This microbial underworld is intrinsically linked to many aspects of life we take for granted. It’s actually a lot more inextricably linked than most of us know or suspect. Studies of mammalian subjects have shown that microbiota are crucial. In fact, axenic mammals fare very poorly in comparison to their microbe infested kin.

I have posted a series of links to articles via my social media about not only the physiological importance of having a microbiota,  but also about how intimately entwined these hitchhikers have become with complex life-including us.

Aphids harbour a bacteria called Buchneria wolbachia…
Shown here residing within bacteriocytes; modified fat cells in the host aphid’s hindgut

At this point in time a great deal of research has been carried out on human microbiota: gastrointestinal,  mouth etc. Of invertebrates, sponges have been the object of most study. 

Sponges have been around for nearly 800 million years, and stand testament to an old adage: if it ain’t broke, don’t fix it.

Big Pharma has taken to the seas in recent years, upon realising it is a treasure trove of bio-active compounds which may be of use in combating disease,  including cancer.
Molluscs have been an increasing avenue of research as the neverending war between modern humanity and disease rages on. A predatory marine whelk; Dicathais orbita has been one such focus of research. This snail produces bio-active compounds believed to have anti-cancer properties.

One interesting aspect of this emphasis on invertebrates as a source of new medicines is that it highlights a possible role for bacteria in production of these compounds. For example, molluscs such as D. orbita are the only molluscs to employ a class of compounds called bromoperoxidases in the production of bio-active compounds. However, gene sequencing of D. orbita has turned up no genes or proteins that synthesise these compounds. Subsequent searches of databases such as NCBI has turned up nearly a hundred bacterial genes for bromoperoxidases. 

Microbiomes (in the case of D. orbita) do exist. Whereas they have been exhaustively catalogued in humans only recently have studies into invertebrates and their structures begun to bear fruit. 

In D. orbita, bacteria show selective colonisation of differing regions within the snail. Certain organs and glands are known to be bio-active; for example rectal and hypobranchial glands. These regions show low diversity of bacterial passengers. In contrast non biosynthetic centres; gut, mantle and foot showed a seemingly random and diverse spread of bacteria. This is easily explained by environmental uptake.

A female specimen of D.orbita. Highlighted (white arrow) are two biosynthetic centres: the hypobranchial gland and rectal gland, both of which show a structured bacterial complement.

This seemingly selective dispersal of differing bacterial spp. suggests mechanisms by which certain bacterial groups favour particular locations within organisms. Once they have taken a hold there they then proceed to earn their keep; in the case of D. orbita providing chemical defences against other bacteria and pathogens. 
Bacteria are supreme opportunists, having been found almost in literally every environment on and under earth. Whereas they have a natural tendency to form semi-structured, semi-organised communities known as biofilms they also just as readily colonise other organisms, co-opting them for shelter and other benefits whilst paying their way. Their role in the rise and continued existence of. multicellular life can not be overstated.