Category: biology

Tuesday, 6 May 2014

08:58 – If someone had asked me to name biotechnology companies, Autodesk wouldn’t have been on my list. Thanks to Brian Bilbrey for this link. As it turns out, Autodesk should have been on my list. They just created a synthetic bacteriophage virus.

Although this is a very fast-changing field and the video linked to in the article is nearly three years old, it’s still worth watching.

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Saturday, 14 January 2012

09:36 – S&P downgraded the sovereign debt of France, Italy, and Spain yesterday, but that may turn out to be yesterday’s second most important eurozone development. Of course, everyone is focused on upcoming debt auctions by those countries over the next two or three weeks, at which they can expect very high yields and very low bid/cover ratios, but the really significant euro news yesterday was the collapse of negotiations on Greek debt.

The “troika” insists on PSI (private-sector involvement), which means there won’t be any more bailout money for Greece unless private investors “voluntarily” agree to a “haircut” (write-down) on the Greek debt they already hold. Yesterday, hopes of that pretty much disappeared. The group representing private investors basically told the troika to get screwed. Why should they take any loss at all? If Greece formally defaults, the credit-default swaps that the private investors hold become payable, and those investors walk away with 100% instead of 50% or less. Of course, there’s also a very high probability that a formal default by Greece causes the collapse of the euro and the eurozone, with Italy, Spain, and the rest toppling like dominoes. As of now, there’s no more bailout money in prospect for Greece, which has debt coming due in a few weeks and no way to finance it. A so-called disorderly default looks almost certain, after which everything quickly unravels.

Yesterday, I decided to do a complete reorganization and rewrite of the final lab session. I had intended to focus that session on vertebrate organs and organ systems, but I finally realized I was trying to cram an entire anatomy book into a single lab session. So instead I’ve repurposed that lab session around an exploration of tissue types, which will of course also touch on numerous organs and organ systems. So, rather than finishing the session today as planned, it looks like it’ll take me a couple more days.

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Thursday, 12 January 2012

08:00 – I finished the lab session on cell-division yesterday and sent it off to my editors. I told Barbara last night that it’s fortunate I work at home alone, or I’d probably have been locked up in a rubber room long ago. Yesterday, I was writing and just started laughing for no reason that would have been apparent to a bystander. Most people wouldn’t find meiosis all that funny.

I’d written about mitosis and decided I’d better include at least an overview of meiosis, a life process with a similar name and similar mechanisms. The difference is that mitosis operating on a diploid cell produces genetically-identical diploid daughter cells, while meiosis produces genetically-unique haploid cells, i.e., gametes. The process by which meiosis produces this genetic uniqueness is called homologous recombination, during which homologous pairs of chromosomes exchange some of their genes.

So, as I was sitting there writing about meiosis, I thought about that immortal phrase that by itself shows the pitiably parlous state of science reporting. A year or so ago, a CBS news story actually used the phrase “homologous recombinaltion tiniker”. (Well, technically a phrase is a group of words, and only one of those three groups of letters is actually a word.) So, for a moment, I actually considered including a graphic titled “Homologous Recombinaltion Tiniker” to illustrate that gene shuffling. That’s when I started to laugh.

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Wednesday, 11 January 2012

08:12 – The guy from Piedmont Natural Gas showed up yesterday to look at the gas logs. He blew out the thermocouple/oxygen sensor mechanism, as I’d done, but apparently more successfully. The pilot light has been burning since he left, but we haven’t had the gas logs lit yet, other than the several minutes that we let them burn while he was here watching them. The pilot flame now looks normal, a pure blue gas flame rather than blue tinged with yellow.

I’m almost finished with Lab IV-3: Investigating Cell Division. That will go off to the editors today, and I’ll jump back into the final session, Lab XI-4: Investigating Vertebrate Structures. I’ll finish that this week, and that’ll be it for new material, other than the Preface and Introduction. I’ll get those knocked out next, and then jump into rewriting and cleaning up the material I’d already written. This book will be ready to go to production on 31 January.

I’ve never yet been happy with a book at the point I have to let go of it and let production do their magic, and this one is no exception. As our friends Mary and Paul can confirm, I’ve been walking around for weeks now, muttering “I HATE biology!” Of course, before that it was “I HATE forensics!” and before that it was “I HATE chemistry!” And I don’t doubt that at some point it’ll be “I HATE physics!”

The good news is that the time between to-production on 31 January and when the book is actually published in April or May gives me a cooling off period. When I finally hold the printed book in my hands, I’ll flip it open to a random page and immediately spot an error. It happens every time. But then I’ll start paging through it and decide, hey, this is actually a pretty good book. That happens every time, too.

09:41 – Well, this is interesting. Italy, which is paying unsustainable interest rates with no relief in sight, has basically told the EU, “give us money or we’ll depart the euro and withdraw from the EU.” Of course, Monti didn’t phrase it exactly that way, but the meaning is clear. If Germany doesn’t pay Italy’s bills, which Germany is not going to do, Italy will leave the EU. And Italy has metric boatload of debt to sell in the near future. It’s paying over 7% now. I shudder to think what it’ll be paying soon.

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Tuesday, 10 January 2012

08:00 – With three weeks until deadline, I’m in the home stretch on the biology book now. I’ve allocated the rest of this week to finishing up two lab sessions that are now in progress, one the vertebrate survey and the other about the life cycle (cell division/mitosis). Once those are complete, I’ll spend a few days doing a quick run-through of all the lab session chapters, cleaning them up and making them consistent before I send them off to reviewers. Then I’ll finish up the Preface and Introduction chapters and start incorporating comments from the editors.

Someone on the Well-Trained Minds forums posted a query yesterday about scanning her old color negatives to produce digital image files. She’d found the Epson Perfection V300 Photo Scanner on for $80 and asked if that would do what she needed. My old Epson 3450 scanner died some time ago, and I’ve had replacing it on my to-do list since then. I checked and found that the V300 is Linux-compatible, so I replied and told her that I’d just ordered one and if she wanted to hold off for a while I’d test it by scanning some of our old color negatives and let her know how it worked.

Barbara is mad at me because of my reaction to a story in the newspaper this morning. Apparently, she was talking about it with her friends at work yesterday. Some woman couldn’t find her dog, so she went and looked in her neighbor’s window–which I’m sure is what any of us would do if we couldn’t find our dogs–and saw him having sex with the dog. They got a DNA sample from the dog, which they had a vet analyze. The DNA matched, so they arrested the guy. When Barbara told me what had happened, I started to laugh. She was not amused. “This isn’t funny!”, she said. “It’s disgusting.” The more I laughed, the more trouble I was in. Must be a girl thing.

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Saturday, 7 January 2012

09:14 – Of course, I couldn’t help myself. When I started thinking yesterday about doing a lab session on mitosis and meiosis, I just had to dive in and get some of my thoughts recorded. I ended up stubbing out that lab session and shooting some images.

That got me thinking about equipment limitations. I was shooting images of a prepared slide of onion root tip mitosis, with several mitotic phases visible in one 400X field of view. I have a truly excellent Chinese microscope, a National Optical model 161 with ASC objectives, but it’s still a Chinese microscope and it still has achromatic objectives. As I was trying to count chromosomes at 1000X, I found myself wondering just how much difference it would make to be using a Zeiss or Leitz model with plan apochromatic objectives. I suspect that detail that was just on the edge of visibility with my microscope would have been clear and easily discriminated with the Zeiss or Leitz scope. Of course, just one objective lens for one of those scopes can cost $5,000 or more, and a complete tricked-out scope with all the options can easily run $50,000.

I just answered a question this morning over on the Well-Trained Minds forum about National Optical microscopes versus no-name/house-branded Chinese microscopes. As usual, a lot of forum members say they bought XXX model and they’re very happy with it. Which is fine. I’m glad they’re happy with what they have, but the reason they’re happy is that they can see something when they look into the eyepiece. They have no basis for comparison, and few of them would know a good microscope if it bit them. If I could sit them down to do a side-by-side comparison among their $250 microscopes, a $500 National Optical scope, and a $5,000 Leitz scope, the scales would fall from their eyes.

Of course, I also recognize that the difference between $250 and $500 may be a deal breaker for a lot of homeschool families. And the truth is that any homeschooler is much better off with whatever microscope they can afford than with no microscope at all. So I suppose I should just shut up about it.

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Wednesday, 14 December 2011

08:06 – I finished the group of lab sessions on Plantae yesterday, and I’m starting on the group on Animalia this morning. That’s the final group. When I finish it, I’ll go back and start “filling in” with additional lab sessions in other groups that I wasn’t sure I’d have time to complete.

So this morning I’m starting on a lab session that covers Porifera (sponges) and Cnidaria (jellyfish, anemones, hydrae, and so on), both phyla that include the simplest animals. After that, I’ll do another lab session on invertebrates–worms, insects, and so on–and then move on to chordates–fish, amphibians, reptiles, and of course mammals.

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Tuesday, 29 November 2011

07:20 – UPS showed up yesterday with a whole bunch of bottles and lids. I shoved them into the spare room that used to be full of computer gear until I have time to move them downstairs.

When we ordered the Pentax K-r DSLR, I was hoping that the Live View feature would make it easier to shoot images through the microscope, and indeed it has. Here’s Aspergillus sp. at 100X showing conidia and spores.

It’s still difficult to achieve proper focus, but much less so than it was without Live View. Without Live View, I often had to shoot literally 30 or 40 images of the same view to get one in reasonably good focus. It’s near impossible to focus on an SLR focusing screen when viewing through a microscope. With Live View, I can generally get a pretty well-focused image by shooting three or four images and tweaking the focus slightly each time.

Of course, the real problem is that for most subjects there’s really no such thing as proper focus, because those subjects are actually three-dimensional. Although many appear to be two-dimensional, most of them actually have depth. It’s often a matter of 100 micrometers or less, but that still means that when one part of the object is in focus, others aren’t, particularly at higher magnifications. Even in this image, which is a thin section at only 100X, some of those tiny little spores are sharply focused and others aren’t. That’s because some of them lie above the plane of focus, and others below.

I’ve often wondered if I should use stacking software designed for astrophotography to shoot composite photomicrographs with everything is in focus. The problem in astrophotography isn’t focus–everything is at infinity–but turbulence in the atmosphere, which changes constantly and blurs parts or all of the object. With stacking software, you shoot many images–hundreds to thousands–and then process them with the stacking software. It finds the non-blurred parts, if any, of each individual image and then combines those into one composite image. Processing an image is, of course, resource intensive, both in terms of disk and CPU. Even a fast PC may need several minutes to many hours to complete the stacking process, depending on image resolution and the number of frames in the sample.

Of course, I wouldn’t shoot dozens to hundreds of photomicrographs separately. Instead, I’d focus the microscope as well as I could and then adjust focus one direction or the other until the image was clearly out of focus I’d then turn on the Pentax K-r video mode and capture 720p video for 30 seconds or a minute as I very slowly ran the focus in the other direction. It’d be an interesting experiment, but of course the results would be low-resolution (720p), probably not good enough for publication. Also, I just don’t have time to do this. Finally, using images that were in sharp focus across the entire field would raise unrealistic expectations among readers, i.e., “What’s wrong with my microscope?”

09:42 – Amazon says they sold four times as many Kindles on Black Friday this year as they did last year. Presumably the same held true yesterday for Cyber Monday. Of course, a lot of those Kindles are Kindle Fires, which I suspect most buyers intend to use primarily as tablets rather than e-readers. Reading ebooks on a backlit display is a miserable experience, as anyone who’s used both backlit LCD and e-Ink readers can tell you. So the reality is that e-reader sales have perhaps only doubled year-on-year, if you consider e-readers to include only devices that people actually use primarily for reading.

Sales of e-readers last December were high enough to cause catastrophic sales declines for print books, particularly MMPBs, which fell about 50% year-on-year. Sales of e-readers this month should be sufficient to pretty much kill MMPB entirely, not to mention driving another nail in the coffin of trade paperbacks and hardbacks. For now, trad publishers are hanging on, although they’re doing so by raping customers with $10 and higher ebook prices and raping authors with 17.5% royalty rates. That won’t go on much longer, as more and more people, both readers and authors, come to understand that even $2.99 is a pretty high price for just a license to read a book, and as more and more titles become readily available on torrents. By this time next year, I suspect a lot of people will be trading multi-gigabyte ebook archives in the same way they started trading MP3 archives years ago.

10:49 – I just got email from a reader asking which Kindle I’d recommend, and why. There’s no single answer to that, so here goes:

If you’re a serious (heavy) reader of novels, no question, the baby Kindle 4 is the best pure ebook reader. At only $79 ($109 without ads), this should be a no-brainer for any serious reader. It’s noticeably smaller and lighter than the other models, so nearly anyone can use it one-handed, and it just gets out of your way while you’re reading. If you take notes, play games, or otherwise use a keyboard or if you want to listen to audio books, this model is a bad choice, but otherwise go for it. The ads, incidentally, are not at all intrusive. You see them only on the screensaver and as a small pane at the bottom of the screen that lists your titles. As regular readers know, I hate and despise ads, and these don’t bother me even slightly.

If you’re a serious fiction reader who does need a keyboard or listens to audio books, go with the Kindle 3. It’s larger and heavier than the baby Kindle and some people will have trouble holding it securely with one hand, but otherwise it’s a match for the baby Kindle except that it has a physical keyboard and audio support.

If you’re looking for a cheap iPad and you intend to use it only casually for reading ebooks, go for the Kindle Fire. Just be aware that, although the Fire is probably about as good for reading ebooks as an iPad, in real terms that means it isn’t very good at all.

Finally, the bastard child, Kindle Touch. This might actually have been my first choice, if only Amazon had included physical page-turn buttons. They didn’t, which means to turn pages you have to move your finger and touch the screen, which really, really gets in the way of reading. Not to mention smearing up the screen. About the best I can say for the Kindle Touch is that its virtual keyboard, which is operated by touching the keys on-screen, is a lot better than the baby Kindle’s virtual keyboard, which requires moving the cursor around using the arrow keys on the controller button. Still, if you need a keyboard, in my opinion the original Kindle 3 (now the Kindle Keyboard), with its physical keyboard, is a much better choice.

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Monday, 28 November 2011

07:02 – Barbara arrived home in the early afternoon yesterday. As usual, Colin and I did our happy dance. One of us was so excited, he peed. I’m not saying which.

I was working on the fungi/lichens chapter yesterday when I nearly took leave of my senses. The “standard” stain for fungi, which also serves as a mounting medium, is called lactophenol cotton blue or LPCB for short. It’s what I would use for staining fungi, no question. There are other stains that work, but not as well.

So, I decided I needed to include LPCB in the biology kit. I actually started tracking down sources for the chemicals and pricing everything. One of the components–phenol, AKA carbolic acid–is tightly regulated by DOT for shipping, so I made sure that I could ship under the small-quantity exemption, which indeed I could. Then I finally came to my senses. Phenol is truly nasty stuff, and LPCB is essentially a 20% solution of phenol in glycerin and lactic acid, with some water and a small amount of dye added. Phenol is highly toxic, absorbed through the skin, and corrosive. Making matters worse, phenol is a local anesthetic, so you don’t even feel it as it eats through your skin and poisons you. Not something I or any sane person wants an inexperienced 15-year-old student messing with.

So, turning lemons into lemonade, I decided to have students test the various other stains already included in the kit to determine their effects on fungi. Safranin O is actually not a bad alternative to LPCB, but I won’t tell them that. Let them find out for themselves.

14:05 – Yesterday I linked to a YouTube version of The British Grenadiers. The Grenadiers were and are scary guys, no doubt about it. Over the last 350 years or so, they’ve helped Britain win more than a few battles. But for some really, really scary guys, check out the Biochemist Grenadiers. These guys and their colleagues in the other sciences win wars and topple empires. You want these guys as friends.

If you’re not a scientist, you may find the lyrics incomprehensible. Don’t worry. It’s not just you. Here a few lines of the lyrics:

The moiety of glucose, in the succeeding phase
Is transferred to a ketose by an isomerase
Phosphofructokinase now, acts on that F6P;
Fructose 1,6 bisphosphate is the product that’s set free.

The kinase is effected quite complicatedly
And as you’ll have suspected it uses ATP;
FBP by aldolase is split reversibly
To phosphoglyceraldehyde, also DHAP.

It’s good to be a geek.

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Saturday, 26 November 2011

09:37 – Barbara is due back tomorrow afternoon, so tonight’s my last chance for wild women and parties. No luck so far.

I’m still working on the chapter on fungi and lichens. I’d forgotten how much I hate biological taxonomy. When Barbara and I were taking biology classes in junior high school, fungi were still classified as plants. Then in 1969 Whittaker proposed the five-kingdom system that put fungi in their own kingdom, which they richly deserved. For the next 20 years, everything went swimmingly well, until DNA analysis pretty much wiped out morphology-based taxonomies, which really messed everything up.

Imagine you had to classify four people under the old morphological taxonomy. Individuals A & B appear Nordic–very light skin, blond hair, blue eyes. Individuals C & D appear sub-Saharan African–very dark skin, brown hair, and brown eyes. Under the obsolete morphology-based taxonomy, individuals A & B clearly belong together, as do individuals C & D. But then DNA analysis comes into play, showing that individuals A & D are more closely related to each other than either is to either B or C, and that individuals B & C are more closely related to each other than either is to either A or D. So, in the new DNA-based taxonomy, individuals A & D are in one group, while individuals B & C are in another group. It makes sense scientifically, but it is non-intuitive to say the least. (Obviously, all four of these individuals are actually members of the same species and subspecies, but the point remains.)

In a more accurate example, fungi have always been considered more closely related to plants than to animals. In fact, most biology books, including recent ones, treat mycology as a sub-discipline of botany. But the reality, based on DNA analysis, is that fungi are much more closely related to animals than they are to plants. Geez.

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