Monthly Archives: February 2013

Hey Hey, it was one year ago today

212-davy-jones-marcia-brady_smwell, tomorrow…

no, that’s not right either.

Well, it was about a year ago that the Monkeys lost their lead singer.




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Posted by on February 28, 2013 in Uncategorized


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Life Revisited: We’re speaking different languages

I know I’ve talked about this before on this blog, but I can’t get my hands on any essays I’ve written about how life is defined and how this question remains a longstanding topic of discussion between me and my wife on what makes something alive.



I feel fairly confident that we both have a pretty good grasp on what the arguments for and against something being called ‘alive’ are. It’s not the characteristics of life that we dispute, but how much weight each of them should carry.



As a bit of background, it should be stated that even biologists have a fairly difficult time defining life formally. Many of us can point to a rock and declare ‘not alive’, to a dog and declare it ‘alive’, etc. But these are simple examples. The things that really challenge the definitions are where details and technicalities become sticking points.

The two standard tests of life can be summarized as:

1. The Cell Theory – The cell is the basic unit of life and therefore all life must be cellular.

2. Defining life as things that have ‘The Characteristics of Life’:

a. Life must be ordered

b. Life must reproduce

c. Life must metabolize

d. Life must be homeostatic

e. Life is evolving

f. Life responds to stimuli

g. Life must grow/ develop

My wife has a much more comprehensive view of what it takes to be called alive. She would like to see most, if not all of the seven characteristics of life fulfilled and also holds to all life being cellular. When pressed, I think that she finds the most value in defining life as those things that can metabolize for themselves. They may require certain environmental support (waters, food, etc.) but when given these things, they can meet all the characteristics of life… but metabolism seems to be one of the most defining of these characteristics.

I’m not sure if holding to this definition represents any specific school of thought, but I suspect it reflects an organismal approach to life informed by her history as a clinician.

I, on the other hand, have a much more minimalistic definition of life that elevates the importance of reproduction over most other characteristics. If a thing has genetic material of some sort and can reproduce this material resulting in new life, that is sufficient for me – even in the absence of many other characteristics from the list above.

Why is this so important to me that reproduction trumps all else? I wasn’t sure what it was until I got to thinking while listening to Richard Dawkins’ newest book, The Magic of Reality. I’m listening to it for a number of reasons, perhaps primarily because I am developing a new course for the Summer semester that examines the philosophy of science. However, Dawkins hits upon many of his standard points in this book, one of which is, ‘we are all simply machines built by our genes, for the sole purpose of perpetuating those genes.’

There it is, a molecular definition of life. A definition, which although I was not always consciously aware of it, was critical to the way I approached biology. In my head, all living things are just self-replicating molecules wrapped in complicated shells (bodies). It’s really just the DNA that is alive.

This is exactly the opposite definition as that held by my wife. She views the organism as a whole as the primary unit, that thing which is really alive. One comment that she made that clarified her perspective to me the most was that it’s really not as important to talk about what is alive and what is not, as it is to talk about what has consciousness and what does not. I think this is really cool, it’s almost like an eighth characteristic: awareness. This is not to say that things cannot be alive just because they are not self-aware, but to add something new and elevate the definition from mere life to something more. Something relatable.

I think it’s important to remember that this is really a philosophical point. As such, the answers are not as easily classified as right or wrong, but merely as points of view.

We have also talked a lot about how language shapes the way people think. We both agree that this is possibly one of the major differences amongst people of various cultures. Some people speak languages that place more or less importance on things (one example we discussed recently was that some languages do not have a future tense that distinguishes it from talk of the present tense. This may impact how certain cultures value the future more or less than others … think saving for retirement). Some people benefit from being multi-lingual and therefore having many frames of reference, or lenses that they can view current events through.



I bring this up because she started her professional career as a veterinarian, caring for animals, curing disease, controlling chronic problems, managing pain. The animal was the focus. I, on the other hand, began my professional career as a molecular biologist, snipping out genes, cloning them and expressing them in different organisms. The genetic material was the focus.

Just like language, our careers shaped our approach to life and allowed us to define it from very different perspectives.

People are funny that way.

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Posted by on February 27, 2013 in Uncategorized


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Jeopardy, coffee and cookies

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Gameboard for tomorrow’s In-class Jeopardy

Now I’ve done it.

I often feel like saying things out loud is a curse against me. I’m expecting to get up early and make some fresh coffee and cookies for tomorrow’s Micro Exam #1 Review.  But, with the curse and all, I do worry…

The one thing I do have going in my favor is a longing for chocolate chip cookies. For some reason I have not been baking as much lately, but I’ve been trying to get back in the habit. The last two weekends I have made bagels though, so perhaps it will happen.

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Bagel Recipe adapted from Laurel’s Kitchen Bread Book

So, tomorrow, after two cancelled classes due to inclement weather:

Micro: Open review of all material, discussion of the next chapter in Vaccinated (hmmm, I’ve lost track of where we are…), quiz on the last chapter of this unit(Ecology, growth and nutrients) and then potential exam question jeopardy.

General Bio: Continue / finish  cell division and cancer (both covered in chapter 5 of the text), then discussion of the latest chapter of Your Inner Fish (again, I’m at a loss. The chapter after teeth…).

I’d get up and check these things, but I am trapped under a large, sleeping cat who is known to be ferocious when disturbed, so I’d rather keep my hands.

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Posted by on February 27, 2013 in Uncategorized


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Science and Communication

'Chemical Lectures', c 1810.It seems like there is a lot of talk about how to talk lately.

Scientists are an interesting bunch. We’re all taught to communicate in a very specific way: Be sparing in what you say, even more sparing in what you claim, assume your audience can recognize the difference between good data and bad and always give them your best, because they’ll call you on anything less, etc, etc.

Then there’s the public. Frankly, not many of us are any good at addressing that audience; it’s large, it’s diverse, not everyone knows how to read your graphs and wants you to shut up for a sec while they work it out themselves, etc, etc.

Yet, science has a lot to communicate with the public. And I think the public would like to address the scientific community once in a while too, but it’s not necessarily any easier to communicate in that direction either (most people don’t look through ncbi to find someone working on the topic they’re interested in learning more about and then finding the corresponding author for a quick email chat. )

There are some books out there, like Randy Olson’s, ‘Don’t be Such a Scientist’ that does a good job of helping scientists see how others like to be communicated with. Recently, at the AAAS meeting (that’s the American Association for the Advancement of Science) had a talk about how to communicate that touched on many of the same points Olson’s book covers. Perhaps most importantly is a group like Sense About Science that attempts to bring peer review to the mass media.I think this could be one of the simplest, and most powerful changes in how science is communicated. This was recently discussed in a Scientific American article outlining the objectives for the group.

Nevertheless, many scientists balk at discussing certain topics in public because it may lend a sense of legitimacy to views that are politically or religiously motivated, rather than scientifically.

What do you think should be done to open lines of communication between scientists and non-scientists – or on how media should be held accountable for providing source data on scientific claims?

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Posted by on February 27, 2013 in Uncategorized


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Although this post is about individual vs group selection theories, I would like to focus on the example put forward. – Why the sex ratio is bound to remain approximately 1:1 in many organisms? I discuss this often in my own general bio class when we come to stabilizing pressure on populations, but I think I will start using this extreme example to make the point even clearer.

Why Evolution Is True

I’m teaching introductory evolution this quarter, and am using as a textbook Doug Futuyma’s Evolution (second edition, Sinauer). Today’s lecture will be on the maintenance of genetic variation via natural selection (heterosis, etc.), and in the textbook under “frequency dependent selection,” I see this on page 319:

Why is the sex ratio about even (1:1) in many species of animals? This is quite a puzzle, because from a group-selectionist perspective, we might expect that a female-biased sex ratio (i.e., production of more females than males) would be advantagesous because such a population could grow more rapidly. [JAC: such a sex-ratio-biased group would then outcompete other groups and predominate]. If sex ratio evolves by individual selection, however, and if all females have the same number of progeny, why should a genotype producing an even sex ratio have an advantage over any other?

The answer, first realized by Ronald Fisher…

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Posted by on February 27, 2013 in Uncategorized


Tuesday Classes

Again, it looks like a major winter storm is coming in just in time to cancel class for tomorrow. We’re under a winter storm warning with the expectation of significant snow accumulation:

from NOAA

Updated Feb 25, 2013, 8:10pm CST





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Posted by on February 25, 2013 in Uncategorized


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Check out this excellent series of micrographs of an onion cell undergoing meiosis to produce pollen. Be sure to check out the descriptions of each phase in the process as you walk through the process. The Prophase2 illustration is difficult to pick out – however, this is reality. To paraphrase Roger Waters “Reality shows what is;Textbooks illustrate what mother nature intended.”

Seeds Aside

Just because people deserve microscopy! Here is illustrated a male meiosis, which produces the four pollen grains, in Allium senescens (Alliaceae, Asparagales). There is nothing like seeing chromosomes or cells dividing… (before I come back into writing stuff).

Male meiosis in A. senescens

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Posted by on February 25, 2013 in Uncategorized


The House Where Darwin Lived

ImageLike a barnacle, Darwin settled into his home not far from Kent, England that is featured in last month’s Smithsonian Magazine.

I have this spot on my science bucket list along with Galapagos, Brno and others.

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Posted by on February 24, 2013 in Uncategorized


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The Human Genome Project as a teenager

Human-Genome-Page-From-BookSeveral classes ago, we were talking about some modern therapies and research being done and I mentioned how the human genome was sequenced in the mid 90s as the world looked on speculating about the wealth of benefits that would ensue. We talked a while about how this sequencing effort gave us some idea of the size of the human genome as well as a number of many other organisms. The one of my students asked what real, clinical good had come from this expense of time, money and effort.

I talked about some of the benefits this information had to basic science and how we were now nearing a time that genome sequencing was becoming feasible as a clinical tool.

Several years ago, during the tenth birthday of the human genome , Nature magazine polled scientists about the importance of knowing the complete sequence of the human genome. At that time, most scientists felt that the most value rom the project was to be found in improvements of the sequencing technology itself and to basic research. Very few researchers thought that clinical medicine was receiving any benefit from the project.1


2010 Nature Magazine Poll of Scientists

A few years ago, this sort of test was so difficult and expensive that it was generally only available to participants in research projects like those sponsored by the National Institutes of Health. But the price has plunged in just a few years from tens of thousands of dollars to around $7,000 to $9,000 for a family. Baylor College of Medicine and a handful of companies are now offering it. Insurers usually pay.2

So, what tangible benefits have been realized?

In my mind, I was thinking of a variety of changes that this had harkened in the research community and how it was a great tool to have a frame of reference for asking questions like, “Do I have any mutations in my proto-oncogenes or tumor suppressor proteins that may lead to cancer?” But I was unaware of any specific anecdote that would put a human face on the story and provide evidence of benefit.

However, I was listening to Science Times, the podcast for the New York Times Science pages on the way to class this morning and I heard just that. This article discusses several of these cases, one with a life-changing positive outcome and another with little tangible benefit as yet.

Perhaps we are starting to see spillover into clinical applications, or perhaps, as Eric Lander, a leader of the Human Genome Project, said today in an interview with WBUR’s Here and Now , it takes decades to see the benefits of breakthrough technology get to the clinic. In that case, this is just the beginning and we have much to look forward to.

In the mean time, go check out the genome data and play around. You never know what you might learn.

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Being Human




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Posted by on February 20, 2013 in Education


Refining the Tree of Life

Image“Therefore I should infer from analogy that probably all the organic beings which have ever lived on this earth have descended from some one primordial form, into which life was first breathed.”

Darwin, Origin of the Species 

One of the basic ideas of biology is Darwin’s notion that all life on this planet is related through common ancestors at some time. It is only though the passage of ‘deep’ time, the infidelity of genetic machinery (among other processes) leading to variation and the separation of species by physical (or other) boundaries that has led to divergence into the great variety of species we see today. Constructing phylogenetic trees is a simple graphical way of communicating this concept.

The Animal Tree of Life, published in the 15 Feb 2013 Science magazine <LINK>discusses the construction of a phylogenetic tree over the past 25 years since molecular evidence was admitted as a means of establishing relationships with greater accuracy, and with less subjectivity than ever before. “  For the past century, the use of detailed descriptions of animal adult morphology and embryology has been at the heart of the study of evolutionary relationships among distant groups such as phyla. However the methodology can have both implicit problems and practical difficulties.”    1

This early paper used 18S rRNA sequences extensively to derive phylogenies because it was thought that this gene was required for life of many (all?) organisms and that sequence was highly critical to an organism’s survival, and would suffer fewer modifications over time than other, less crucial genes.

The earlier disagreements derived from varying interpretations of the morphological and embryological characteristics of animals. Many of these characters have evolved repeatedly in unrelated lineages as adaptations to similar selective pressures or have been lost from certain groups through disuse. Today’s strengthening consensus is almost entirely thanks to the use of molecular genetic data in reconstructing trees. Heritable changes in nucleotides and amino acids are abundant and generally much less prone to the problems of convergent evolution and loss than are morphological characters.2


More recently, sequencing of mitochondrial and chloroplast DNA has revealed these organelles’ relationship to free-living bacteria, providing an interesting challenge for illustrators of these genetic trees and establishing solid data supporting the endosymbiotic theory.

Using the great wealth of DNA data we have today, relationships can be determined using similarities found in a number of different genes, providing a high degree of statistical assurance that the conclusions are unbiased and accurate.



1. K. G. Fieldet al., Science 239, 748 (1988).

2. M. J. Telford, R. R. Copley, Trends Genet. 27, 186 (2011).

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Posted by on February 19, 2013 in Uncategorized


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