Nitpicky terminology distinction

Minor point that I wanted to clarify for the benefit of all, since a student just brought it up to me.

When we take pictures of stuff we see on the microscope, it’s called photomicrography. We are taking photomicrographs, or photographs of microscopic object.

It is not microphotography. A microphotograph is a teeny-tiny little picture, a small picture of a larger object. You’d need a hand lens to see a microphotograph.

OK? Just a little peeve. You’ll sometimes see people using the two terms interchangeably. They are bad people who must be crushed immediately, their remains scuffed into the dust, and their names obliterated from all stelae and funerary urns.

I do photomicrography, and have never ever done microphotography (which is a real thing, it’s just not what microscopists do.) If you need help remembering the distinction, just remember my initials are PM, and I do PhotoMicrography. So you don’t get pissmisticated when you make a horrible gaffe in front of me.

(The student got it right, by the way, and so I allowed them to live.)

What I’m also going to teach today: a little image processing

My development class also has a lab. The last few weeks have all been teaching them how to get good optics on a research scope, and how to take photomicrographs with my PixeLink camera system. Today I’m going to show them how to appropriately process an image for publication, so they’ll learn a few digital enhancement tricks and a few ethical rules. I lay down a few laws about using image processing on scientific data:

What you must do to your image:

  • You must archive the original data and work with a copy. If I ask to see the original after you’ve enhanced the image up the wazoo, you better be able to show it.

  • You must document every step and every modification you make. You’re going to describe everything either on the image itself or in a figure legend; if this were to be published, you’d probably include it in the Methods section.

  • You must explain the scale and orientation of the image. The scale is usually shown by including a scale bar; orientation may be shown either by including annotations (text describing landmarks in the image) or an explanation in the figure legend, such as that it is a sagittal or horizontal section.

  • You must save the image in a lossless format, such as .png or .psd or .tiff. Do not save it in a lossy format like .jpeg, which can add compression artifacts.

What you may do to your image:

  • You may crop and rotate the image.

  • You may adjust the contrast and brightness for the whole image.

  • You may carry out simple enhancements, like applying a sharpening filter or unsharp masking, to the whole image…but remember, document everything!

  • You may splice multiple images together to produce a photomontage; you can also insert panels with enlarged or otherwise enhanced regions of the image, as long as it is absolutely clear what you’ve done.

What you may not do to your image:

  • You must not carry out selective modifications of portions of the image; you cannot sharpen the cell you care about and then reduce the contrast for other regions, for instance. You should not burn or dodge regions of the image.

  • No pixel operations or retouching: you are not allowed to go into the image and paint your data into existence!

We do a lot of this preliminary basic stuff because I run the course out of my research lab, rather than a student lab. I want to make sure they’re not going to break anything, and also that they know how to do good imaging, a skill they’ll find useful in other courses and in research (years ago when I taught this stuff, we’d also do black&white darkroom work — nobody does that any more, so now it’s all photoshop). The goal is to get them all able to churn out lovely photographic data, so later I can just hand them some nematodes or fruit fly embryos and tell them to do their own experiments and observations, just show me the pretty pictures when they’re done.

It’s a good life, being able to sit back and let students bring me gifts of biological beauty. I think they’ll also be posting some of these to their blogs.

What I taught today: gene regulation and signaling

Today was more context and a bit of a caution for my developmental biology course. I warned them that we’d be primarily talking about animals and plants (and mostly animals at that), but that actually, all of the general processes we’re describing are found in bacteria and other single-celled organisms — that in a lot of ways, microbiology is actually another developmental biology course. Yes, I went there: developmental biologists tend to be imperialists who see all the other sciences as mere subsets of the one true science. Of course, you could also take that as developmental biology being a synthetic discipline that steals bits and pieces from everywhere…

So the primary lessons today were reviews of stuff these students should have gotten in cell and molecular biology, with bits of biochemistry and microbiology thrown in. We talked about genes getting switched on and off, and the example I used was the classic: the lac operon in E. coli. What? You don’t know about it? It’s a beautiful system, in which the bacterium switches on the genes needed for digesting the sugar lactose only when the sugar is available in the environment. I showed this nice little 3 minute video:

Switching genes on and off? That’s development! It gets a little more intricate in multicellular animals, but all of the fundamental logic is right there in E. coli: activators and repressors, positive and negative feedback, the boolean logic of gene regulation. I also mentioned that when we’re reading Carroll’s Endless Forms Most Beautiful, he’s going to make a big deal out of exactly this kind of regulation, but I want them to remember that it’s not unique to butterflies or fruit flies or frogs, it’s a common theme in all kinds of diverse cells.

We then talked about cell signaling. How does a cell know which genes are supposed to be off and on? It interacts with its environment (as in the lac operon) or its neighbors to make decisions about activity. To illustrate that, we went through quorum sensing and biofilms — again, cell signaling is not unique to animal development, it was all worked out in principle in single-celled organisms. I gave them a little foreshadowing and mentioned that we’d be discussing Sonic Hedgehog and Notch and Delta later in the course, classic examples of signaling in multicellular systems, but in bacteria we have things like hapR and AHL signaling.

Finally, I raised the issue of a phenomenon we’ll be talking about on Wednesday: patterning. Why aren’t your arms growing from your hips, why don’t you have fingers on your feet instead of toes, why are your eyes paired and on the front of your head? Because there is positional information in the embryo that can be read by cells and tissues and lead to development of appropriate structures in their proper places. But once more, this is not unique to multicellular animals. A paramecium, for instance, is not a generic blob, but has a definite shape and orientation; it has organelles in predictable places, and is covered with a nearly crystalline lattice of cilia with specific axes of orientation. I showed them choanoflagellates and pointed out that these protists, representing a multicellular precursor, had a specific shape and a collar organ in a specific functional location: how do they know how to do that?

That’s the question we’ll be asking next. I warned them too that I won’t be lecturing at them on Wednesday, so they’d better have their morning coffee. I’m expecting them to read a review paper on positional information in embryos (pdf), and I’m going to make them explain it all to me for a change.

Slides for this talk (pdf)

For Wednesday:

Kerszberg M, Wolpert L (2007) Specifying Positional Information in the Embryo: Looking Beyond Morphogens. Cell 130(2):205–209.

#giantsquid time!

I’ve fired up the television and am tuned to the Discovery Channel. What is this godawful crap about rednecks and moonshine leading in to the documentary on the giant squid? It does not bode well.

Ooh, they’re teasing us with short clips right at the very beginning. Good start. Less “monster” talk would be welcome, and more biology and ecology would be welcome.

Boy, they really threw money at this project: multiple submersibles, multiple film crews, cameras all over the place. Also infrared lighting, which accounts for the appearance of some of the video previews.

I would like to know what the recipe for that gloppy squid lure Steve O’Shea is mixing up. He calls it a squid “aphrodisiac”…and he tasted it. Squid breath!

Ah, the aphrodisiac is squid bits run through a blender, a squid milkshake. Do not try something analogous if you are looking for a human aphrodisiac.

Hmm. They’re kind of setting this up as a conflict between the three scientists involved — Widder, O’Shea, and Kubodera, and portraying O’Shea as ‘controversial’. Really? We’ll see if there’s any real drama or if this is exaggerated and contrived (I suspect the latter).

Real science is often tedious. This show is just giving us the highlights — O’Shea just went on a 7 hour dive in a submersible, we got to see a couple of brief shots of some lovely jellyfish and a couple of small squid (which were nice!)

I guess this is build up. 45 minutes in, we’ve seen all three scientists do a dive, and all three fail. That’s OK, I think they’re illustrating how science is done about as effectively as you can with a television entertainment.

This so reminds me of going fishing, trying different lures semi-randomly to find out what they’re biting.

Oh, wait, they are fishing!

I’ve been watching for an hour and ten minutes, and they finally flash a glimpse of a large squid at us. Need…more…data. Getting a little thin here.

It figures. All the people hanging about underwater in submersibles…nada. Unmanned probe left to record unmonitored for 30 consecutive hours…success!

It is now sinking in that that 30 seconds of a giant squid lunging at a robot probe has been padded out to an hour and a half. It’s spectacular footage, but there really isn’t that much of it.

OK, stop this. Last 15 minutes seem to be solid commercials interlaced with one minute segments of documentary. This is getting ridiculous.

Finally! A giant squid just hangs onto some bait while brightly lit for 23 minutes…and they show us about a minute of it. Why not just drop that fluff and have the last half hour be nothing but continuous footage of the 26 foot long beast hanging there? That’s what I want!

My final assessment: mixed. They got some really, really good video, but apparently they didn’t think it was enough, and so they padded it out way too much. There were some half-assed attempts at the beginning to play up conflict and drama between the researchers, but they didn’t pan out and weren’t at all relevant; the stuff about “monsters” was distracting; the occasional attempts to compare this search to bigfoot, UFOs, and the Loch Ness monster — only real — was just annoying. There was some promising set up of the methodology, but not enough about the biology.

The people who made the show clearly didn’t think just the video footage of the squid was sufficiently engaging. They were wrong. They also clearly felt a need to milk it for every penny of commercial time they could get.

I look forward to when just the raw footage of the squid is released. That’s what I want to see.

An important warning regarding your household recreational drug use

I  try not to abuse my soapbox here by proselytizing too often, given that this is a topic on which hordelings have deeply divided points of view. But sometimes a warning is just far too important not to share.

I’m not moralizing here. What you do with your own body is between you, your conscience, and your connection. But an informed choice is always the best choice. I urge you to pay close attention to this Public Service Announcement.

Science doesn’t say that!

Have you ever noticed how the religious regard ‘scientism’ and ‘reductionism’ and demands for concrete evidence as barely a notch above obscenities? That is, until they need to reduce complex issues to simplistic claims and don the mantle of Science to support their beliefs. Then they become Holy Writ.

You can really see this behavior in the abortion debate, where suddenly anti-choicers decide that humanity is defined by a particular arrangement of alleles in the genome. Case closed, they say, Science has spoken! Unfortunately, they get the science wrong, and we know their commitment to the authority of sacred science will be discarded the instant a scientist says something they disagree with…like, say, there is no soul and the mind is a product of the brain, or you are an evolved variant of an ape, or maybe, just maybe, genes aren’t the magic ju-ju beans you think they are.

A classic example was published in the Independent. Look how Declan Ganley bows and scrapes to the authority of science, multiple times!

Of course, the only way to guarantee that the law protects all individual members of the human species equally, is that at a minimum, from the moment that a member can be identified as such, the law insures immunity from deliberate bodily destruction.

This moment of identity is unequivocally known today as conception (as indeed the word itself suggests), when the DNA of a new member of the human species arises. It is scientifically indisputable that the DNA discovered here by science is that of a unique individual distinct from their biological mother, and that this DNA is the unique and irreplicable identifier of a unique member of our species.

So the question is not whether we know when the human individual is first created (this is unequivocally proven by science), but rather whether an individual’s right to life can be made subject to another and one individual human can be fully owned by another to the point where their very life is subject only to the whims of another.

None of us are created in the fullness of our potential, but science has shown us that human life is a journey, not a static moment. Our potential is gifted us at our conception – our appearance, talents and very fingerprints are hardcoded, and the rest is up to us. We are all conceived with the destiny to be born, grow, mature, slowly fade and die. The deliberate and targeted interruption of this process at any point is the ending of a single, unique, never-to-be-replaced human existence, and is the most base form of discrimination. That is why we make killing another human the most serious of all the crimes.

I’ve got news for you, Ganley. Science does not have such unambiguous answers as you claim; human-ness is an emergent property of a gradual process of development, and no one is going to ever be able to say, “Here, right here, is the magic instant in which an embryo becomes fully human.” That’s because “human” as used in law and sociology and philosophy and even theology is something complex and very, very hard to define, so looking for a mathematically precise and sharp boundary in the vagueness of complexity is a contradiction in terms.

You can try to do it by putting on blinders and pretending that the genetic sequence of an individual is sole criterion, and that it is well-defined and unambiguous, but it isn’t. It just creates more problems.

Genetically, we’re nearly identical to chimpanzees. They have the same genes in roughly the same organization on their chromosomes; they have some novel variants, or alleles, but every newborn chimp also has a “unique and irreplicable” arrangement of alleles. Why aren’t you declaring their lives precious and demanding protection? Why not say the same for cows and ears of corn? They are also genetically special.

But, you will say, they are uniquely human. And I will ask what that means. If I have a mutant gene (and I do! On average, I’ll carry a few hundred novel mutations relative to my parents) that isn’t shared between me and all other humans, am I still human? If I have a cytologically detectable chromosomal rearrangement, am I still human? How many differences are allowed between two genomes before you can say one is not of the same species as the other? Is an embryo with a unique deletion in one chromosome still human? If an embryo has a unique mutation that makes it infertile as an adult when interbreeding with other members of the species, is it still human?

That magic line in development should be getting a bit smearier in your head about now. Conception isn’t necessarily associated with the generation of a unique person.

I’m glad that he noticed that science sees development as a journey, but a little disappointed that he couldn’t see that that actually contradicts his claims about conception as a singularity. Just the genetic complement is not enough. A blastocyst, a hollow ball of cells with an inner mass that will become the embryo proper, has exactly the same genes as a five year old person or an octagenerian. But it doesn’t have limbs or eyes or brain, it doesn’t think or feel, it doesn’t dance or learn. It is…a hollow ball of cells. It’s got cilia and might spin in place. That’s about it. It’s human only the most trivial, reductionist sense.

That should tell you something. There has to be something more. There has to be a complex history of epigenetic interactions that set up tissue domains and generate morphology and trigger physiologically functional activity in different cells. That isn’t there yet. That history is a significant part of what makes you what you are right now, and it’s absurd to pretend that that doesn’t matter and that everything is plainly established at the moment of conception.

And of course, he’s factually wrong. To claim that “appearance, talents and very fingerprints are hardcoded” is not true, and all you have to do is look at identical twins to see that it is false. There is a good similarity in appearance, but if you know any identical twins at all well, you know that you can tell them apart…and that their differences increase with age. I’ve known a few elderly identical twins, and you wouldn’t know that they were identical unless you’d been told so, because variation accumulates. “Talent” is also meaningless; there is evidence that some broad characteristics (musical ability, for instance) are heritable, but so much of what we call “talent” is not intrinsic, but the product of hard work and discipline.

Also, fingerprints are not hardcoded. Identical twins have general similarities in the arrangements of whorls and loops, but are readily distinguishable in the details.

Science would not belittle the significance of all the essential changes that go on after conception, so I think Mr Ganley was a bit premature in claiming its authority for his dogma. How about if we recognize instead that science actually tells us that the process, that journey he regards as so vital, is the interesting part, and that imposing arbitrary dividing lines on a continuum is a silly exercise that he’s trying to use to put boundaries where there are none?