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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.

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 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.

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Posted by on February 14, 2014 in Uncategorized

 

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First Day: In the Can

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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:

 
 

85

 
 

92

 
 

90

 
 

74

 
 

102

 
 

90

 
 

83

 
 

77

 
 

76

 
 

83

 

 

  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

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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,

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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.

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                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?

 
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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.

also,

“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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