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Monthly Archives: November 2012
RadioLab’s Inheritance Podcast
My son and I just listened to a completely engrossing podcast on inheritance from RadioLab. The episode had three stories about different aspects of inheritance and genetic control. The first didn’t capture my interest nearly as much as the next two, so I won’t discuss it here.
The second story proposed and interesting idea of Lamarckean inheritance based on the extraordinary record-keeping of a far-north town in Sweden. In this town, the church kept amazingly detailed records about births, deaths, disease, health and even crop production year to year. When all these data were analyzed, researchers found a strong correlation between the availability of food to men in the village and the health and wellbeing of that man’s children. What might seem unintuitive is that contrary to what you might think, the children of men who suffered through years of starvation when they were ~9-12 years old fared the best. If dad ate well, your health prognosis was poor. If dad ate poorly, your prognosis was better. The effect even seemed to trace down two generations.
The explanation for this was that at this time in a man’s life he is making the cells that will go on to make sperm. Somehow, these cells can receive genetic imprinting that improves the fitness of the offspring.
Let me stop here. I have to say, I think this is entirely unconvincing. I can think of at least one simpler explanation for these data. Further, I can easily imagine how if it was possible to turn on these beneficial changes, evolution would make this the norm rather than the exception.
Example data. A) Population lifespan following feast years, 100% survival. B) Population lifespan following famine years, 50% survival.
Consider a population of 100 kids in the target age group during a year of ‘feast.’ 100% of these kids survive and have children. These children have an average lifespan of 50yrs. Given the same group during a year of ‘famine.’ 50% of the kids survive and have children. The children live to an average age of 75 yrs. It appears that the famine during the elder generation improved the fitness of the younger.
But, if we examine the ‘feast’ population again, we might see that they can be broken up into two natural groups, one with a 75yr lifespan (the healthier 50%) and one with a 25yr lifespan (the less healthy). If the famine year selectively kills the weaker kids, then we are simply selecting our way to better health rather than causing it.
Because this is published research I expect that this simple answer was excluded somehow and I hope to find the original work to see that, but the burden of proof rests on the group proposing the more complex explanation.
I’ll see if I can research this a little and write again later, but I wanted to comment right away because I thought that it was an interesting example of how numbers can sometimes lead you astray if you’re not careful.
Oh, and very quickly, the last story…
The last story was about a woman who had adopted a baby girl, Destiny, from a mother who was addicted to drugs and couldn’t support the child. Amazingly, the next three years after that, the same mother gave birth to three more addicted babies that were all adopted by the same family. Because of her frustration about how this woman was so casually bringing more children into the world, one a year, each addicted to heroin et al. at the time of birth, the adoptive mother tried to pass a law to somehow prevent this from happening. When that failed, she worked directly to set up a fund to pay addicted women to undergo surgical sterilization or get long term birth control.
Many saw this as eugenics in action. Personally, I see no convincing connection to eugenics whatsoever based on the fact that the procedure was voluntary and based on a behavior rather than an innate characteristic of the women. Nevertheless, the conversation went places I never expected – mostly because I thought Jad and Robert would not get drawn into such ridiculous speculations and extensions of logic as they did. It was still good listening though.
I highly recommend checking out this episode.
HHMI site
I just completed a survey on the HHMI website that introduced me to some of their resources that I have not yet explored. One that I thought was relevant to our current work is on chromosomes, genes and sex determination. It can be found here.
Follow this link to the BioInteractive Animation Page where you can find the animations of DNA Replication, Transcription and Translation (among others) that we watched and discussed in class.
DNA Replication
DNA Replication occurs during the S (Synthesis) phase of cell cycle. The purpose of DNA replication is to create an identical copy of all the DNA in the cell so that, following cell division, both daughter cells will have complete copies of all the information required to build a cell and do all the things the cell does.
Data from several laboratories were elegantly integrated by the work of Watson and Crick to describe the structure of DNA as comprised of two anti-parallel strands bound together by polar (hydrogen) bonds between one purine and one pyrimidine. Including:
1. Erwin Chargaff ‘s observations that
a) DNA was 50% purine (A and G) and 50% Pyrimidine (C and T) and
b) the proportion of A = the proportion of T; the proportion of C = the proportion of G .
2. Rosalind Franklin’s X ray crystallography data that indicated that DNA had a regular, repeating pattern and the molecule was of a specific width.
3. Oswald Avery’s group along with Hershey and Chase established that DNA was the genetic material (therefore making the structure of this molecule of high importance)
4. Knowledge of the distance between molecules engaged in hydrogen bonds.
5. Knowledge of the chemical properties of nucleotide molecules, comprised of hydrophilic deoxyribose sugars and phosphate groups and hydrophobic bases.
Altogether, this information provided enough background for the pair of researchers to arrive at the structure of DNA by engaging in model building.
How this all leads into the mechanism of DNA replication comes down to the following brief statement at the end of Watson and Crick’s Seminal Paper of the structure of DNA:
“It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.”1
What did they mean by this?
“The novel feature of this structure is the manner in which the two chains are held together by the purine and pyrimidine bases…joined together in pairs, a single base from one chain being hydrogen-bonded to a single base from the other chain… [O]nly specific pairs can bond together. These pairs are: adenine…with thymine…, and guanine… with cytosine.”1
So, if the sequence of DNA bases on one strand dictates the sequence of the other, then each of the strands can be used as a template to make another. When this is done with each of the two strands, the result is two identical DNA molecules.
It’s one thing to say that it hasn’t escaped your notice that there is a mechanism for duplicating DNA inherent in its structure, but quite another to say that you know how it works.
This was the question that Matthew Meselson and Franklin Stahl were to solve in 1958.2 They imagined three possibilities:
- A Conservative method of replication – the original DNA splits open and new strands are made based on that information, then the original strands comes back together and the new strands zip together. We conserve both strands of the original copy.
- A Semi-Conservative method of replication – The original DNA splits open and new strands are synthesized to pair with each of the originals, the new DNA then exists with one original strand and one new one.
- A Non-Conservative / Dispersive method of replication – Frankly, I don’t know how this would work, but the result would be two new DNA molecules where bits of each strand of each molecule may be from the original or the new DNA.
How to distinguish between these methods?
Meselson and Stahl devised an experiment that in which they grew the bacteria, E. coli in broth containing DNA made of two different isotopes of Nitrogen. In one broth, let’s call it the ‘light’ broth, they had the light form of DNA with 14N, in the other, ‘heavy’ broth, they had the heavy form of DNA with 15N.
One really is heavier than the other. When they are centrifuged, they will come to rest at different ‘heights’ in the tube.
If the bacteria is grown in broth containing only the heavy DNA, and that DNA is harvested and spun down, you would see a tube like (a) containing a single band of the heavy DNA.
If than bacteria was moved into a new medium containing light DNA, and DNA was allowed to replicate once,
Assuming semi-conservative or dispersive models of development – you would see (b) a single band of intermediate density – because all new DNA would be partly heavy and partly light.
Assuming the conservative model – you would see (c) two distinct bands – one heavy and one light.
So this immediately tests for or against the conservative model.
The actual result was a single intermediate band was found. This eliminates the conservative model of replication, but a second round of replication in the light broth is required to discriminate between those two models.
If the Semi-Conservative model is correct, then the intermediate band would remain, but a new light band would show up (d).
If the Dispersive model is correct, then the intermediate band would inch upwards (become lighter) as more light elements are mixed in randomly within the strands. (e)
What they found was exactly like that pictured in figure d. Further, if the bacteria were allowed to grow for more generations, the ‘light’ band of DNA would become larger as more light DNA is created, while the intermediate band will remain indefinitely.
Meselson and Stahl with Chase
References
- Watson. J. D. and Crick F.H.C. “A Structure for Deoxyribose Nucleic Acid” Nature 171, 737-738 (1953).
- Meselson, M. and Stahl, F.W. (1958). “The Replication of DNA in Escherichia coli”. PNAS 44: 671–82.
Wired Article about EteRNA
Citizen Scientists
I forgot… I meant to post a link to an article written in Wired magazine about the EteRNA RNA folding game. It’s an interesting look into how crowdsourcing is beginning to make inroads into science and how clever gamification turns readers into players and puts them to work on deciphering some of the largest data-heavy / problem-solving questions in science. Find that article here, or you can also find the actual magazine at FSCC in the hallway magazine shelf.
Link
–>James Watson on Discovering the Structure of DNA<–
This week we will be starting to discuss the molecular basis of inheritance in class.
Watch as Nobel Laureate James Watson relates the story of the discovery of DNA’s structure. One clear distinction that can be seen between good scientists and extraordinary scientists is the ability to see the big picture. Consider this idea as you listen to his story.
EteRNA
I meant to mention in class that I wanted anyone who is interested to check out EteRNA online over the holiday. We are going to be talking about DNA, RNA and Proteins again in chapter 25 and EteRNA is an interesting game that gives players a look into the world of RNA folding. I will mention this again in class this week, but if anyone wants to check it out, I will award a ’10’ on the chapter 25 quiz to the player with the highest score by that time.
Who said what about the molecular basis of inheritance? First steps towards the double helix
A workable Theory
Gregor Mendel did the first documented, accurate analysis of how one generation inherits traits from their parents’. However, being so far ahead of his time, and possibly because he may have been considered an outsider to the scientific community, the value of his work was not grasped and it was quickly forgotten. Mendel had stated a couple of theories in his paper making theoretical assumptions of how ‘factors’ responsible for inheritance are segregated during the formation of gametes and then rejoined in the zygote. Together, the two factors that every individual had for each trait determined the expression of that trait.
Colorful Bodies
From Zellsubstanz, Kern und Zelltheilung, 1882
A couple decades later Walther Flemming observed, under his microscope, some curious movements of things called ‘chromosomes’ (or colorful bodies). Unfortunately, he did so without knowledge of Mendel’s work and thus didn’t recognize the greater meaning of his discovery. At this time Germ Plasm Theory (not to be confused with Germ Theory) was being debated as a means of inheritance. This theory suggested that special germ cells carried the hereditary material from one generation to the next and that these cells were uninfluenced by the other cells of the body. The plasm itself took the place of Mendel’s idea of factors, but functioned as a more inclusive measure of material, more akin to what we call the genome today. I say ‘plasm’ is replacing ‘factors’, but it should be noted that no one intentionally renamed Mendel’s factors. The real problem was that no one knew about his work at all.
Edouard Van Beneden had been investigating similar chromosomal movements during meiosis that produced the gametes, or germ cells. However, he too was having a difficult time constructing a cogent theory concerning how these movements led to inheritance.
August Weismann
August Weismann was in the best position at the time to put the pieces together as he was already turning the available information over in his mind to construct a big picture. He recognized that the nucleus was the likely source of the ‘plasm’ and even considered the chromosomes as a possible candidate for this material. Further, he was concerned with how it was that germ cells could join in a way that did not double the heritable material with every generation.
Connecting the Dots
It was not until Sutton and Boveri independently unearthed Mendel’s work and recognized the similarity of chromosome movement during gametogenesis (making sperm and egg cells) to his descriptions of ‘factors’ that The Chromosomal Theory of Inheritance was first seriously proposed.
Altogether, these observations led many to believe that it was, indeed, the chromosomes that carried the genetic material. Still, this did not pinpoint what molecule was responsible or how it accomplished this for chromosomes are comprised of long strings of DNA and a number of proteins. Given the simplicity of DNA, many refuted this as potential genetic material as it simply could not carry the required information. Perhaps it served as a scaffold for the more important protein molecules? This was consistent with the chromosomal theory and had the benefit of allowing for complicated proteins to bear the information required to build new cells and organisms.
Griffith with his pal Bobby
Fredrick Griffith was one of the earliest workers to begin the march to identify the specific molecules that functioned as heritable material. While working to develop a vaccine against Streptococcus pneumoniae, he discovered their curious capacity for communicating information laterally, from one organism to another.
Griffith’s Experiments: Glimpsing the Answer
Two forms of the bacteria were known: One a virulent smooth form that secreted a protective carbohydrate capsule, and Secondly, a rough strain that lacks this protective coating and is non-virulent. Predictably, mice he infected with the smooth strain died as a result of bacterial overgrowth. Mice infected with the rough strain overcame the infection and lived. Also, as one would predict, heat-killed bacteria of both strains had no ill effect on mice. But what Griffith did next was much more interesting…
He took heat killed smooth bacteria and combined it with the non-virulent rough form and found that the resulting cocktail of bacteria not only killed mice, but these mice were also found to be overgrown with the smooth form of the bacteria.
What are the possible explanations?
- The S strain can come back to life in the presence of R strain bacteria.
- Some information was taken up by the live R strain bacteria that allowed it to take on a trait from the dead S strain bacteria.
Griffith chose the simpler second option and suggested that some transforming factor was responsible. This factor was released by the dead S strain and carried heritable information.
Unfortunately, Griffith wasn’t around long enough to see the story play out as he perished during the German air raids of London during WWII. But one last experiment done by another group illustrated that he was one the right path. This experiment repeated Griffith’s work carefully, but instead of combining S strain and R strain bacteria, the S strain bacteria were spun down into a pellet using a centrifuge and only the liquid supernatant was moved in with the R strain bacteria. As Griffith might have suggested, this liquid carried his transforming factor and was sufficient to cause a change in the R strain to make it produce and secrete the carbohydrate capsule.
This last experiment and some others were done by the laboratory of Avery, MacLeod and McCarty at the Rockefeller Institute in New York and will have to be discussed in a future post.
Get Down
Get Down with Education and download a free copy of The Thirteenth Labor of Heracles free this weekend in the US iTunes store. (by the way, if readers in any other country would like a free download, I’d be happy to extend our thanksgiving ‘sale’ to you.)
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