Archive for the 'Biology' category

SPSP 2013 Contributed Papers: Computation and Simulation

SPSP 2013 Contributed Papers: Computation and Simulation

Tweeted from the 4th biennial conference of the Society for Philosophy of Science in Practice in Toronto, Ontario, Canada, on June 29, 2013, during Concurrent Sessions VII

  1. First up, Catherine Stinson, "Computational models as experimental systems" #SPSP2013 #SPSP2013Toronto

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SPSP 2013 Plenary session #3: James Griesemer

SPSP 2013 Plenary session #3: James Griesemer

Tweeted from the 4th biennial conference of the Society for Philosophy of Science in Practice in Toronto, Ontario, Canada, on June 28, 2013.

  1. Getting set for Plenary 3 at #SPSP2013 #SPSP2013Toronto which will be James Griesemer, "Model Taxa as Platforms for Biological Research"
  2. That there's a story (and a set of tweets) for Plenary 1 and also for Plenary 3 raises an obvious question:
  3. "Why no tweets for Plenary 2?" you ask? Because my laptop was used by the esteemed Rachel Ankeny for her slides #SPSP2013 #SPSP2013Toronto
  4. Assisting the speaker in achieving the conditions required to project her slides is a good thing, yes?
  5. Have taken notes in the quad-rule notebook for sessions not tweeted. Will try to tweet or blog them when I can #SPSP2013 #SPSP2013Toronto

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SPSP 2013 Symposium S10: Talking Junk about Transposons: Levels of selection and conceptions of functionality in...

SPSP 2013 Symposium S10: Talking Junk about Transposons: Levels of selection and conceptions of functionality in...

Tweeted from the 4th biennial conference of the Society for Philosophy of Science in Practice in Toronto, Ontario, Canada, on June 28, 2013, during Concurrent Sessions V

  1. As an audience member in this session, I had much less relevant background knowledge than I did in some others.  But I was pretty aware, from goings on in the science blogosphere, that there has been some amount of disagreement about what to say about "junk DNA," the ENCODE project's findings, and the coverage of it all by science journalists.
  2. Waiting for Symposium on "Talking Junk abt Trasposons: Levels of Selection & conceptions of functionality..." #SPSP2013 #SPSP2013Toronto
  3. First up: T. Ryan Gregory, "Junk and the genome" #SPSP2013 #SPSP2013Toronto

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SPSP 2013 Contributed Papers: Explanation in the Biological Sciences

Jun 28 2013 Published by under Biology, Conferences, Methodology, Philosophy

SPSP 2013 Contributed Papers: Explanation in the Biological Sciences

Tweeted from the 4th biennial conference of the Society for Philosophy of Science in Practice in Toronto, Ontario, Canada, on June 27, 2013, during Concurrent Sessions III

  1. Again, I had to make a choice about which of four sessions to attend, and this one drew me in.

    You might ask, "What happened to Concurrent Sessions II?"
  2. I know my multi-tasking limits, yo!
  3. On deck: session of contributed papers on explanation in the biological sciences. #SPSP2013 #SPSP2013Toronto
  4. First up: Ingo Brigandt, "Systems biology & the limits of philosophical accounts of mechanistic explanation" #SPSP2013 #SPSP2013Toronto

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Friday Sprog Blogging: paleozoic poetry

A little early this year, the elder Free-Ride offspring wrote these "sci-kus" for science class. They're like haikus, except with a few more syllables per line (7-9-7* rather than 5-7-5), because the names of geological periods require more syllables.

* * * * *

Cambrian oceans were full
Of sponges, trilobites, and snails
Invertebrate paradise

Ordovician fishes
Were the first, and coexisted with
Crinoids and cephalopods

Silurian plants survive
On land, and in the seas, fish with jaws
Have made themselves known to us

Devonian forests
Made up of ferns and conifers
Situated on land

Tree ferns, amphibians,
And insects in Carboniferous
Became the coal of today

At the end of Permian
Mass extinction of the sea's creatures
Farewell, sweet amphibians

*Two of these are actually 7-8-7. I'm guessing poetic license (or perhaps poetic learner's permit).

Wouldn't it be cool if they had the equivalent of driver's ed for poetry? What would they show instead of Red Asphalt to scare the kids off reckless poetry?

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Friday Sprog Blogging: You call this living?

As I mentioned on the Twitters, when, upon my return from ScienceOnline 2012, my family members hit me with the question, "What did you get me?" they were thrilled that the answer included science-y watercolors by Michele Banks (who, by the way, has a show ongoing).

Science watercolors by Michele Banks

My favorite is this cute phage, not least because it prompted a conversation between the Free-Ride offspring.

Phage watercolor by Michele Banks

Dr. Free-Ride: Isn't this cool?

Younger offspring: It looks like a bug with a balloon on its butt.

Elder offspring: No, it's a phage.

Younger offspring: What's a phage?

Elder offspring: It's a virus that eats bacteria.

Younger offspring: Aren't viruses and bacteria the same thing? Don't they both make you sick?

Dr. Free-Ride: Well, viruses and bacteria both fit in the category of "germs".

Younger offspring: Don't they both make you sick? Isn't bacteria the same level of bad as viruses? And why would a virus eat a bacteria? Wouldn't that make the virus sick?

Dr. Free-Ride: There are some bacteria that are totally benign that are probably living in your intestine right now, without which you would have a hard time getting all the vitamins you need, for example. So, there are some bacteria that actually do good work for you.

Younger offspring: Oh.

Dr. Free-Ride: But there are definitely other bacteria that can make you sick.

Elder offspring: Like E. coli for bladder infections.

Dr. Free-Ride: Yeah.

Younger offspring: TMI.*

Dr. Free-Ride: To be fair, some of the bacteria that are in you, doing fine without making your life miserable, are E. coli. It's particular strains of E. coli that can make you sick.

Younger offspring: Isn't it bacterium?

Dr. Free-Ride: Yes, bacterium is the singular, bacteria is the plural. So ... what's the difference between a bacterium and a virus?

Elder offspring: A virus isn't really living. The only thing that it does that is similar to living things is reproduce, and it doesn't do that by itself -- it needs a bacterium to reproduce.

Dr. Free-Ride: Say more about that. Is it like a photocopier, which reproduces but needs someone to push the button?

Younger offspring: Wait, if bacteria can help viruses reproduce, isn't that another way for bacteria to hurt us?

Elder offspring: It's not like the bacteria are doing it by choice!

Dr. Free-Ride: They are sort of being commandeered by the viruses, aren't they?

Elder offspring: Yeah. The viruses just attach on and then insert their genetic material.

Dr. Free-Ride: And say, "Hey, bacterium ..."

Elder offspring: "... do THIS instead of your normal life functions!"

Dr. Free-Ride: So, instead of your normal life functions, make more of the stuff that I've shot into you, which is basically virus-stuff?

Elder offspring: Yeah. And then when the bacterium gets too full of viruses? It goes BOOM! and all the viruses go find new homes.

Dr. Free-Ride: It explodes like an overheated spaghetti squash.**

Younger offspring: That wasn't really needed.

Dr. Free-Ride: Well, you know, sometimes it's good to have a mental image. OK, back to your claims that viruses aren't alive. Strictly speaking, we humans need other stuff in our environment to conduct our life functions. I'm always curious about how we decide where to draw the line between what counts as being a living thing and what doesn't. And I'll bet there are probably some people who think that viruses ought to be on the "living" side of the line rather than the "non-living" side. What's the justification for keeping viruses out of the club?

Elder offspring: They can't produce energy by themselves.

Dr. Free-Ride: Whereas you can? Didn't you recently have a conversation with an organelle that pointed out your shortcomings in this area?

Elder offspring: They can't produce energy by way of mitochondria or whatnot.

Dr. Free-Ride: Ohhh, so because we have mitochondria, we can lord it over the viruses? You think having mitochondria is a requirement for being alive?

Elder offspring: No, you just need to produce energy from something to be alive. Just reproducing yourself isn't enough. I'm pretty sure viruses don't get energy, they just reproduce.

Dr. Free-Ride: Wouldn't that suggest that they're even more advanced than us "living things" in that they don't need energy? I mean, they don't have to stop to eat. They're very nose to the grindstone, achieving the task at hand of making more of them.

Younger offspring: Except that viruses don't have noses.

Dr. Free-Ride: Think of how much more you could get done if you didn't have to stop to eat.

Elder offspring: But then I'd miss all the prettiful flavors.***

Dr. Free-Ride: For that matter, think of how many more of you there could be running around if you displayed the virus' seriousness of purpose about making more of you.

Elder offspring: Ewwww. No.

Dr. Free-Ride: No, not in one of those bizarre animal kingdom kind of reproduction methods. We're talking about you harnessing bacteria to multiply your genetic material.

Elder offspring: Yeah ... still no. One of me is enough.

Younger offspring: Yes it is.

Glaring ensued. As it does.
*Let the record reflect that the younger Free-Ride offspring was objecting to the general information that bladders can be infected, not objecting to an overshare of personal information (and indeed, it was general, not personal, information the elder Free-Ride offspring was sharing here).

**We did this accidentally not too long ago. It blew the door of the microwave oven open in spectacular fashion. It was still pretty tasty, and no one was hurt.

***In case you were wondering, this is a discussion that happened at the dinner table during dinner.

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Friday Sprog Blogging: Interview with a Chloroplast.

Jan 13 2012 Published by under Biology, Kids and science

Yes, it's been a while. This week, I was able to have enough of a conversation with the elder Free-Ride offspring to discover a homework assignment that looked ... a lot like a conversation about science.

In this case, it's a conversation between the elder Free-Ride offspring ("Me") and a chloroplast ("Chloroplast"). Big ups to my child's science teacher for giving assignments that can generate content for this blog (and for letting kids type their homework so I can copy the file rather than having to transcribe).

Me: So, what exactly are you?

Chloroplast: I am an organelle found in the cytoplasm of plant cells and a few kinds of bacteria.

Me: How many of you are there per cell?

Chloroplast: It depends on the organism. There are about thirty to forty of me per leaf cell, but in a certain type of single-celled alga, there is only one of me.

Me: What do you do for the organisms you are a part of?

Chloroplast: I capture the energy of the sun and use that energy, along with some carbon dioxide and water, to make glucose for the cell.

Me: Wow, that's amazing! Is that the process that plants use to make their own food?

Chloroplast: Yes, it is. That process is called photosynthesis.

Me: Is it anything like making a sandwich?

Chloroplast: What!? No! Of course not!!!

Me: Did I offend you? Or do you just not care for a nice, delicious BLT?

Chloroplast: Of COURSE you offended me! We chloroplasts don't use other organisms to make food! And especially not organisms that contain other chloroplasts!

Me: Okay, I'm sorry. How do you cook up some glucose in place of a sandwich?

Chloroplast: It's more like engineering than cooking, you know. First, I store energy from the sun and obtain six molecules each of carbon dioxide and water.

Me: How do you get the water?

Chloroplast: It's carried up to the leaves, where I live with my fellow chloroplasts, by the roots. Now, as I was saying, once I get those compounds, I use the light energy to remove their bonds. Then, I rearrange the elements and make them into a glucose molecules and six O² molecules. The glucose is used by the cell for its daily functions, and the oxygen is expelled from the plant by the leaf's stomata.

Me: Whoa! I didn't know that plants did chemistry!

Chloroplast: Believe it. Bask in our autotrophic glory, you inferior heterotroph.

Me: By the way, you do know that cooking is just a form of chemistry-

Chloroplast: Shut up.

Me: Okay, another question. Are all organelles as rude as the chloroplasts, or is it a unique feature?

Chloroplast: It's not at all unique. You should hear the nucleus sometime.

Me: Now then, I've been wondering about this. How do you absorb the light energy?

Chloroplast: I have a green pigment inside me called chlorophyll. It absorbs red and blue light. Chlorophyll is what turns plants a lovely shade of green, and not your ugly human skin tone.

Me: I have something else to do now. Thank you for your time.

Chloroplast: Wait! I'm not done gloating about my other superior features!

Me: Too bad. Good bye, you jerkwad of an organelle.

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Friday Sprog Blogging: How Well Does Mold Form in Different Conditions? (A science fair project)

The science fair happened, and the younger Free-Ride offspring's project board is now home. (The teachers are still judging and grading the sixth grade projects, which means that the elder Free-Ride offspring's project board is still at school.)

Here, in pictures, are the highlights of the younger Free-Ride offspring's project:

A straightforward descriptive title. (The kid may have a future writing scientific journal articles.)

Gotta have hypotheses to test.

The equipment was not terribly fancy. Then again, except for the bread, it was stuff we already had on hand, which is a plus.

Maybe it's just me, but I always like it when science fair results depart from initial expectations. It makes it feel more like real science, I guess.

The science fair instructions from the school were emphatic that kids should not bring in potentially biohazardous specimens with their projects (and mold was among the things specifically mentioned in the "NO!" list), so the younger Free-Ride offspring took pictures. It may have been smelly, but the range of colors of mold that grew is actually kind of impressive.

My favorite part of the younger Free-Ride offspring's project is the data visualization. For each of the specimens that grew mold in each set of experimental conditions, the kid measured the mold spots (in square centimeters) and added up the total molded area on each data-collection day. Data was collected until each bread sample was totally molded over.

To generate these graphs, the younger Free-Ride offspring calculated the mean mold area for each given type of bread in a particular set of conditions on a particular day. Since each of the bread samples was 4 x 5 centimeters, the younger Free-Ride offspring drew a 4 x 5 rectangle to represent the bread sample and then plotted the average mold growth by filling in the appropriate number of squares. You can see as you go across the plots from left to right that ady by more and more squares get filled in until all 20 are filled, representing complete mold coverage.

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Friday Sprog Blogging: science fair research in progress.

We're less than two weeks out from our elementary school science fair, which means that both Free-Ride offspring are in serious data collection mode. As they look ahead to having enough data to present and "analyze" (you lose points if there's not some kind of computing of a mean, preferably accompanied by bar graphs -- heaven help the child exploring a question which yields qualitative results), I figured we should check in with some notes from the experimental trenches.

The younger Free-Ride offspring has been studying mold-growth on a selection of breads under various conditions (including exposure to light, air flow, moisture, and temperature).

Mold has grown (and on some but not all of the samples -- so there will be differences to explain). Quantifying the amount of mold that has grown on a sample (either by counting wee spots or by using a ruler to measure moldy regions) and recording those data in the lab notebook takes rather longer than the younger Free-Ride offspring had anticipated. Also, while the younger Free-Ride offspring digs wearing the powdered latex gloves to handle the bread samples, the fact that the moldy bread has a distinctive (and unpleasant) odor was a complete surprise.

Dr. Free-Ride's better half is concerned that this is evidence that we have sheltered our kids from the normal operations of the natural world.

The elder Free-Ride offspring's study of whether a rabbit (this rabbit) relies more on sight or smell to locate treats hit a little bit of a snag. The original experiment involved putting treats (or non-treats) in hard plastic vessels --some of them clear, others not, some with slots in them (making it possible to smell what's inside the container), others completely sealed up -- and to observe and record Snowflake's reaction.

From those early trials, we learned that Snowflake was pretty quick in her assessment that she couldn't get inside those containers herself. Secure in that knowledge, she would give up and start munching the timothy hay in her run. Moreover, she discovered that within about 15 minutes of her giving up, the elder Free-Ride offspring would also give up and remove those annoyingly impossible containers from the run -- often giving the rabbit one of the treats when the containers were extracted.

Clearly, the rabbit was too smart for the original experimental design.

However, within the last week the elder Free-Ride offspring has been constructing mini bales of timothy hay, some with treats in them and some not, and has observed Snowflake's differential reaction to them. Ultimately, the data analysis here may require coming up with a scale of smelliness (i.e., of how easy or hard particular treats are to smell). We'll see how that goes.

Meanwhile, I'm making sure both Free-Ride offspring consult literature relevant to the systems they are studying. And I'm getting a new can of spray adhesive so that the display-board assembly proceed without incident.

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Friday Sprog Blogging scary repost: bloody minded.

Oct 29 2010 Published by under Biology, Book review, Kids and science

There are plenty of thrills and chills around Casa Free-Ride these days. Sadly, most of them involve stacks of exams and the horrifying spectacle of a wordy nine-year-old trying to write a concise summary of a 28 chapter book. While we get our diabolical workloads under control, here's a post from the archives appropriate to the spooky season:

Elder offspring: Blood is cool.

Younger offspring: (Covering head with blanket) I hate blood, because I hate owies!

Dr. Free-Ride: But your blood does all sorts of good things for your body. You know that you're filled with blood, right?

Elder offspring: Actually, your body is two-thirds water.

Dr. Free-Ride: And what do you think there's lots of in blood?

Elder offspring: Oh yeah, water.

Younger offspring: I hate blood. I wish I didn't have any.

Dr. Free-Ride: You need it to get oxygen to all the parts of the body.

Younger offspring: No I don't, I'll just breathe harder.

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The sprogs recommend:

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