Tag Archives: life

I love having a blackboard in my home office

In class this week we are discussing genes alleles homologous genes between species and pseudogenes. In order to organize my thoughts (to the extent that I can), I sketched out this diagram to model the flow of information from DNA into proteins and tie this together with the idea that DNA undergoes mutations from time to time and that these mutations are the source of new alleles in the population.


 1.Recall the central dogma

DNA –> RNA –> Protein

Information flows from the DNA out of the nucleus giving rise to proteins that make up the body and do its work. For EVERY gene, you have two alleles, one from mom, one from dad. We tend to only talk about the ones that give us distinct traits that we can see from the outside, but every gene these.

2. Mutations are altered forms leading to altered function

All genes are subject to mutations. Mutations may change the protein that the gene encodes or not. In cases when it does change the protein, we may see a change in function (Form dictates Function). Once we have two different versions of a gene that remain for any period of time, we call these forms alleles of the gene.

3. Interaction of Alleles

Mutations result in these new alleles that may function differently. This may manifest in a form of dominance. If one allele codes for a protein and a second suffered a mutation such that no protein is made, we may look for the protein and say that the form that makes the protein is dominant because one copy should be sufficient to get it made.

4. How can Alleles become Pseudogenes?

Sometimes, genes mutate into a nonfunctional allele that has no impact on the organism (e.g. vitamin C synthesis is not required when the animal eats sufficient vitamin C) in this case, there will be no selective pressure against the non-functional allele resulting in more mutations occurring without consequence. Over time, these alleles can be made completely non-functional.  Pseudogenes are the remnants of these old genes that we can find in the DNA, but that are no longer functional due to an accumulation of mutations. (Only if both copies are mutated and there is no functional copy of the gene in the population do we can this a pseudogene).

5. Speciation and Relationships

As time passes, and speciation occurs, we can still see similarities between the genes of the descendent species, whether these are functional, or sometimes even when they are non-functional. My analyzing the similarities between shared genes, it is possible to infer some relationships between species and even quantitate these relationships in a way that can be used to construct a phylogenetic tree.



Posted by on February 14, 2014 in Uncategorized


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First Day: In the Can


I’m referring to the 2nd definition in this link

I was worried, but I think things went well for my first day of classes this semester. This Spring I am teaching my standard Microbiology course as well as a new Ecology course that I am using to teach all the things that I have never managed to squeeze into my normal General-  and Micro- biology classes.

So far I’m still trying to figure out a way that I can move my Micro class as quickly as possible into Immunology – which is my true love in biology. 

In Ecology, we jumped right into the idea of science as a tool for understanding the universe and working on some of the basic mathematics that help us feel comfortable in the conclusions at which we arrive.  

To describe this, we invented ‘VitaMax!’- a name so absurd that I thought I was inventing it, but it turns out that it’s a real thing – actually a couple of them. Who knew? Vitamax, the dietary supplement,  a multi-vitamin for Cystic Fibrosis patients, a green coffee extract for weight loss, and “A single capsule [that] guarantees firm and lasting erections 45 minutes after being taken.”

(by the way,  is it that a single capsule that gets you multiple erections?)

Well, our VitaMax! extends life … or at least that’s what we’re hoping. The data is in and we just need to evaluate whether it meets our strict requirements before getting it on the market.

Here’s the skinny:

VitaMax!® – Live life to the Max!

Without VitaMax, patients have a normal life span.

  1. Look this up and cite your source. If you are male, use the male life expectancy; if you’re female, use the female life expectancy. Assume the following data matches your ‘control’ group.
    1. Life Expectancy__________________

With VitaMax, patients lived:


life expectancy with Vita-Max:























  1. Determine the mean age patients lived to with VitaMax:_________________


  1. Determine the standard deviation of these patients:______________________



  1. Graph your data as either a bar graph or scatter plot.
  2. Look up a formula for computing Z-Score:


  1. What does Z-Score tell us?



  1. Assuming you can use the SD of your patients as representative for that in both the control and experimental group,  compute the Z-score for the average age without VitaMax __________________


  1. How likely is it that this average age without the drug falls within the area of the bell curve described by your experimental group’s data?


  1. Thinking as a scientist, how would you present this data to your company? Try to make a one-sentence statement about its efficacy.


10. Thinking as a marketing person, how would you pitch VitaMax to the public (without lying)? Try to make this also a one-sentence statement .

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Posted by on January 14, 2014 in Uncategorized


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The 11th item on my (fictional) bucket list


The Bucket

This is another post suggested by WordPress’ 365 Days of Writing Prompts .

A Bucket List. I suppose I have one, but I have no idea what’s on it.

In fact, the more I think about it, the worse it gets. What are the types of things people put on their bucket lists?

Are they noble deeds? … Invite a homeless family over from a shelter and into our house for a Sunday meal?

Should they sounds more like a mid life crisis notebook? … Buy a Porsche 944 as a daily driver?

Should they be like New Years’ Resolutions?… Places I would like to go? Get in shape? Run an Ironman?

What I don’t want is to hear that all these questions are things I need to work out for myself.  I’ve seen the movie. I don’t think I’m going to reform my life by learning that the coffee I like is recycled monkey dung and that I need a best friend or assistant to carry my ashes to the top of K2.

If I have to invest a little grey matter into the question, I would realize that the idea of this question is two-fold: 1 – to generate a bucket list of life’s goals. 2 – to take an easy one and tick it off. Or, at least make a plan to.

Of course, there is a website for creating a bucketlist, but it’s a lot of things that I’m not really that excited about. Mostly bungee jumping, meet Mike Tyson and other greasy kids’ stuff.

The things I would like to do some day are like:

I.              Masochistic notions

  1. Spend a season in Antarctica near Mt. Terror and Mt. Erebus.
  2. Drive across Siberia
  3. Hike across Antarctica
  4. Hike to the North Pole or perhaps sail the NorthWest Passage (sadly, there is one now)
  5. Spend a season in Antarctica near Mt. Terror and Mt. Erebus.

II.            Self Improvement

  1. Learn to code (and prove it by building an app, multifunctional website, etc)
  2. Learn a language well enough to not have someone insist that we just speak English
  3. Publish a book (vanity press / self publishing does not count)
  4. Buy and work on a project car (learn to do what it takes to get this done without outsourcing everything)
  5. Make a noticeable difference in someone’s life (a la It’s a Wonderful Life – in a manner of speaking)

III.          Get a real job where I can feel like I am challenging myself, doing something creative that I can do better than just any teenager off the street and earn enough so I don’t feel like a waste of potential.

  1. (I guess that about covers it … and this one’s #11)

And yet, through all of it, remember the worlds of Albert Camus, “You will never be happy if you continue to search for what happiness consists of. You will never live if you are looking for the meaning of life.”

So, don’t actually think about the bucket.

Just do it?


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Posted by on January 3, 2014 in Uncategorized


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I Think… but I do not Know

Darwin, wrote in his ‘B’ notebook in 1837,


And in one instant transformed the way that we all think about life on earth. This simple diagram unified science. It captured Linnaeus’ nomenclature and married it to the fossil progressions that geologist the world over were seeing in the rocks. It redefined how we understand species and laid the framework for a new view of life as being all related at some level, with some organisms sharing more characteristics with their closer relatives and less with those more distant. It allowed scientists more than a hundred years later to recognize that the biochemical foundations of bacteria and yeast and drosophila and humans were all the same. Because we are fundamentally one family. There was no need to identify a genetic code for each species. Instead, we share a common (universal) code of DNA triplets each calling for an Amino Acid in building proteins.

However, there has been a lot of thought about what it really does mean to be a species. Darwin’s book, The Origin of Species, addresses just this point. I raise this question on the first day of my general biology class and my microbiology class. In general biology we eventually rest on the idea that, at least in the larger plants and animals we are used to encountering – and will discuss in the course of our class, the ability to mate with, and produce fertile offspring from is necessary and sufficient to group two animals into the same species. Of course the mule comes up as a near exception necessitating the ‘produce fertile offspring’ clause, but this is a definition we can accept. In microbiology, we are forced, by the nature of the organisms we study, to discard that convenient description. Many micro-organisms replicate asexually and are capable of transferring genes horizontally.

thrashing fish
knowing they’re in a bucket
and not knowing

          -Issa 1819

In the November 1 issue of The Scientist, Axel G. Rossberg, Tim Rogers, and Alan J. McKane tackle the very existence of ‘species.’ Therein, they acknowledge the fact that we use the concept of ‘species’ for our own convenience and consider the possibility (or rater, probability) that the very idea of species delineation may be artificial. The article looks into the variety of life and how the definition must change depending upon the organisms in question and makes us face the assumptions we often take for granted. Click on ‘The Scientist’ below to see the full article.


                Link to the article in The Scientist

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Posted by on November 27, 2013 in Uncategorized


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Cellular robotics? A cute video summarizing cellular functions from TedEd

Check out this video. I think I like it, but I’m not positive yet. It’s so well done that I’m kind of taken by the aesthetics, however, I’m not sure that this makes cell biology easier to understand. What’s your opinion?


Posted by on November 25, 2013 in Uncategorized


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Inspired by my favorite This American Life, replayed this week

imagesThis comes from the superpowers episode of This American Life. It’s always been a favorite of mine – I probably talk about this episode more than all other combined.

Click here to go to the TAL page

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Posted by on October 21, 2013 in Uncategorized


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RNA World and the Origin of Life

In 2011  Martin Hanczyc delivered a TED talk in London on the topic of the origin of life, “The Line Between Life and Not-Life” that discussed some of his work with proto-cells. I participated in some online commenting on the TED page including a conversation about the origin of genetic material.

I wanted to point to the talk itself and include some of the posts below.

ImageFrom Ted Mozer III: ” Two questions about life and the origin of same on earth:
Is all know life on earth related and DNA (or even RNA) based?
If life was created on earth (and not from a seed that either arrived via an comet or the like or from an alien visit), why is the creation process a not a contining process. Did the creation process occur and then stop once life awoke? If so, why??”

My Reply: “You’re asking a very good question, Ted.
Think of it this way, imagine that life first originated by self-replicating molecules (probably RNAs) that found a nice safe home in some protocells that were floating around in the neighborhood – it doesn’t matter if this is absolutely true or not, just consider the abstract idea. The ‘food’ that these cells need is more RNA and cell membrane material, right? So, the things that these cells will ‘eat’ are exactly the same stuff that they, themselves, once were. If our new cells are successful, they are probably gobbling up all the other pro to-life material around them.
This does not mean that life could not have happened more than once, but if it’s a rare enough event, then the first things to get there are going to probably stay at the top of the heap.

It would be really cool to find organisms that use different genetic material – this would support multiple origin events, but so far, the universality of DNA argues that it was a one-off thing.”

A Comment by an unknown person: “Self replicating RNA? RNA and its components are difficult to synthesize in a laboratory under the best of conditions, much less out in a primordial mud puddle. This is highly unlikely. Yes, this was a miraculous “one-off thing.””

My Reply: “Yes, I agree, it is difficult to conceive of RNA as a self-replicating genetic material that also acts as an enzyme. Although RNA does currently act as genetic material, this role is restricted to viruses while DNA plays the major role of genetic material in all other organisms (including some viruses). Also, much of the enzymatic work in biological systems is currently carried out by enzyme proteins. However, there are still some RNA enzymes (ribozymes) extant, one of note is the ribosome – a protein / ribozyme complex with deep phylogenetic roots.

The idea of an RNA world as life’s origin has been around for some time, with suggestions of such an origin being proposed by Francis Crick, Alexander Rich and Harold White (among others) in the 1960s and 1970s.

Over the years, data has emerged supporting such a possibility including:

“The system, created by Gerald Joyce and Tracey Lincoln at the Scripps research institute in La Jolla, California, involves a cross-replicating pair of ribozymes (RNA enzymes), each about 70 nucleotides long, which catalyse each other’s synthesis.  So the ‘left’ ribozyme templates the synthesis of the ‘right’, which in turn templates the ‘left’ and so on, building each other via Watson-Crick base pairing. “

discussed in “Chemists edge closer to recreating early life”, Royal Society of Chemistry 2009.


“Clemens Richert and colleagues at the University of Karlsruhe have now shown that, without the use of enzymes, an RNA strand bound to a longer template strand of RNA can grow more than one order of magnitude faster than previously believed. This growth occurs in single nucleotide steps according to the base pairing rules of Watson and Crick.”

-From “Accelerating non-enzymatic RNA replication“, Royal Society of Chemistry 2005.

However, support is not proof. There will never be proof of what actually happened, but, then again, I might just be a brain floating in a jar somewhere…

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Posted by on October 13, 2013 in Uncategorized


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“Life is nothing but an electron looking for a place to rest”

ImagePhysics -> Chemistry -> Biology

The Smithsonian Magazine has an article this week proposing that we consider Mars as the origin of Terrestrial Life. This notion stems from Steven Benner’s Four Paradoxes: The Tar Paradox, The Water Paradox, The Single Biopolymer Paradox and The Probability Paradox. Each of these is described in the abstract of his work, and do add up to a possible alternative for life’s origin. However, as compelling as his arguments may be, the origin of life will always be a mystery veiled in time. Even if we were to find evidence of life on Mars that is very much like that on Earth, it would be difficult to say whether Terrestrial life was the origin of Martian life, or vice versa.

Another problem I have with tracing the origins of life off-planet is that it does not solve anything, but merely relocates the source. So it’s not that I feel that Benner’s work is uninteresting or unworthy of consideration, but presently, Ockham’s razor precludes Imageseriously considering extra-terrestrial origins without a good deal more hard evidence. Further,  relocating the source or life’s origin does little to change how we think about  origins. Regardless or where life started, it is still highly probably that it began with RNA, a unique molecule in that even today it serves dual roles as an information-carrying molecule and a structural one that often has enzymatic function. And, that the addition of the more stable , DNA molecule as the primary source of information happened later – as adding protein synthesis also did for providing an alternative structural / functional molecule. 

Evolution of the Central Dogma?


                        DNA -> RNA                                                  RNA -> Protein

                                                  DNA -> RNA -> Protein


Posted by on August 31, 2013 in Uncategorized


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Radiometric dating


An old Rock

My General Biology class is discussing means by which we can date objects. This comes from a question by Ernst Mayr, “What kind of world do we live in?” The basis of this question is, how old is the planet? and how constant is it?

In biology these questions have notable importance because how we explain life’s processes requires that we know how much time these processes are operating over. One would be limited in their explanation of life if we know the world to be young – say, only 1 million years old. Whereas, the current estimate of 4.5 billion years, including ~3.5 billion years with life of some kind, allows for much slower processes to operate.

I discussed one of these measurements, radiometric dating, in an earlier post.  Take a look at how this is done and be sure that you understand the practice problem presented and can work out a similar problem on your own for the quiz.

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Posted by on April 9, 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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