Tag Archives: time

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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TED Talks, free speech and scientific integrity

Screen Shot 2013-03-07 at 3.15.39 PMThere’s a fascinating, fast-moving discussion join on right now sparked by a recent TEDx talk. If you aren’t aware of TED talks, take some time and check them out, they’re a fascinating group of short talks that cover a variety of ideas. Under the TED umbrella, there are also TEDx talks (TED-liscenced talks that are like the parent, TED talks, but more widespread and under less scrutiny), there are TEDed videos that provide short, educational videos targeting classroom use, etc. I’ve been a big fan of TED because of the caliber or speakers and the quality of their talks.

However, one talk has stood out and has received a lot of attention from the scientific community. This came to my attention recently because I follow Jerry Coyne’s blog and he posted the talk in one of his entries along with a strong critique of the talk. You can check out his post here.

Fortunately, and to the credit of TED, this critique has been taken very seriously and the TED site now has an open comment section where the value of this post is being discussed. If you are interested in thinking about what science is… what evidence is … you might like reading through the extensive comments that have simply exploded. As of right now, there doesn’t appear to be much flaming going on and there are some very good comments being made about what it means to do science.

I’ve had conflicting thoughts about whether to bring this discussion up here, because I think the talk is simply terrible in its treatment of science and I was worried that readers might be mistakenly wooed down the garden path by his wonderful oratory skills, but I think the comments section adds enough balance to the discussion and  the holes in his logic are laid bare.

Happy reading.

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Posted by on March 7, 2013 in Uncategorized


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I need a to-do list.Image

My wife took the boy out for the morning, leaving me home alone to work and my brain fried. I have so many things I want to do, it was overwhelming. 

‘The time is gone…Thought I’d something more to say.’

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Posted by on July 15, 2012 in Personal Life


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