June 18th, 2009 ecoli
Daniel Hamermesh on Freakonomics blog links to a study, which shows that states that relax their helmet laws (for bicycles and motorcycles) have more organs available for transplantation.
This is an interesting concept to consider. Should politicians repeal helmet laws, knowing full well that the vehicle operator is fully responsible for their own health and safety, or is the simple change of the law enough to provide incentive signals. Maybe we’d see an increase in the number of people on the organ donation list and their families targeting unhelmetted bike riders on the street with their cars.
Posted in economics., medicine | 17 Comments »
June 14th, 2009 ecoli
Describing a model of infectious disease, as done in the field of mathematical epidemiology, helps scientists and doctors maximize the effectiveness while lowering cost of treating a population of individuals. To do this, however, one must first be able to describe how an infection moves through a population or, more accurately, how the population changes over time due to infectious agents.
This has been done using dynamic differential equation models for a long time now (and they can get quite complex). The most common of these models is called the SIR model (which stands for Susceptible -> Infected -> Recovered) representing the dynamic conditions of individuals within a general population as they “flow through” these different disease states at various rates.
The first ‘discovers’ of the simple SIR model was W. O. Kermack and A. G. McKendrick in 1927, in a paper published in the Proceedings of the Royal society of London. Their model is, ex post, appropriately titled The Kermack-McKendrick model.
The paper itself goes through some complex derivations but the results are suprisingly simple and intuitive. In a closed population, N, where there is no population growth, they assume instantaneous disease incubation, homogeneous population with no age, spatial, or social structure and fixed transmission and recovery rates. The result is this:
The susceptible population, which is the total population at t=0, decreases as an infection spreads and individuals become infected. This occurs at the constant rate of β as a function of the number of infected individuals (the source of new infections) times the number of susceptible individuals (where the infectious agents are spreading to). This means that to sustain an epidemic a disease requires a healthy reservoir of susceptibles or risk “burning” itself out. This equation looks like this:
The dynamics of the infected population depends on the growth of new infections minus the recovery rate (or even death rate) or infected individuals, in much the same way that was described for the change in susceptible population:
Finally, the infected population recovers at a constant rate, γ, at some fraction of the population.
They get a pretty simple model, which they solve mathematically, but, with all these assumptions, can they get any useful data?
Yes!
If you can’t read the chart’s description, this is an epidemic of the plauge on the “Island of Bombay” which fits the The Kermack-McKendrick model for epidemics quite precisely. When the infection gets introduced, although there are plenty of susceptible individuals around, the infection grows slowly (because the number of infected individuals starts out small). However, the exponential trend takes off as the disease creates many new infections (which in turns create more new infections) . But then the disease level crashes as it runs out of new individuals, as individuals recover or, in this case, they die. Whereupon the epidemic is over.
Can we describe or predict the time evolution of an epidemic in a more general way?
Yes (according to the Kermack-McKendrick model)!
The so-called time evolution of the model is described by the so-called epidemiological threshold:
Ro can be thought of as the ‘potential’ for new infections, or the number of secondary infections caused by a primary infection. When Ro < 1, the number of secondary infections is falling, and so the infection is dying out. When Ro > 1 each infected individual will infect more than 1 other person, thereby causing the infection to spread positively within a population.
This quantity Ro (the details of which differ depending on the specific model being used) has been described as one of the most important variables in epidemeology, with consideration for disease transmission potential and therefore disease evolution (in more complex considerations).
Despite the fact that the model’s assumptions may not accurately reflect most real human diseases, Kermack and McKendrick come up with genuinely interesting and relevant conclusions. They find that a population level requires some threshhold value in order for an epidemic to occur, a population size under this threshhold (which is disease specific) will not experience and epidemic. An infection in a population that exceeds this threshhold will reduce the populationas far below the threshhold as it was above it. Small increases in the infectivity rate can lead to dramatic changes in the dynamics of an epidemic, making them stronger. Epidemics generally end well before the entire population of susceptibles has been exhausted. Similar results are seen for diseases transmitted through an intermediate host (like vector bourne diseases).
Although this differential equation model lacks the accuracy of more complex models which relax assumptions and new types of stochastic models, the field of epidemeology has a lot to thank Kermack and McKendrick, for basically creating a new branch, bridging biology, mathematics and medicine.
Posted in classic science, mathematics, medicine, microbiology | 30 Comments »
June 1st, 2009 ecoli
Americans are perfectly split on providing ‘universal’ health care, according to this CNN poll.
H/T – Greg Mankiw
Posted in medicine | No Comments »
May 26th, 2009 ecoli
As someone who is about to lose their previous form of health care insurance coverage, I thought the front page “conversation” on scienceblogs is appropriate.
I don’t want to get into the specifics of the debate, but I thought it was especially interesting that the overwhelming perspective on scienceblogs.com is from the left ‘pro-universal’ side. What is it that makes scientists particularly liberal, especially on this issue? Consider that the economics of the issue is far from settled and that scientists are intimately familiar with the darkside of government funding.
Posted in link out, medicine, musings | No Comments »
April 13th, 2009 ecoli
From Dr. Jekyll & Mrs. Hyde
I have been spending off hours on PubMed, trying to discover the rational basis for the host of rules pregnant women are adjured to obey:
–Don’t eat unpasteurized cheese (Brie, Gorgonzola, feta, chevre…all the good stuff)
–Don’t eat deli meats unless they’ve been heated to steaming
–Don’t even think about licking the bowl clean of cookie batter
–Sushi? Do you want the baby to die, or what?
–Lying on your back past the fourth month is going to give the critter brain damage
–A sip of wine? Why not just smoke crack and be done with it?
I’m not talking “old wives’ tales your grandmother produces.” These things are specifically listed as fetal death-traps in publications ranging from the leaflets I was handed at the ob-gyn to “What to Expect When You’re Expecting,” probably the single most popular pregnancy book available.
But here’s the funny thing. When you look for actual studies about these things on PubMed, you keep thinking that you’ve entered the wrong search terms, because so little comes up.
Expectant mothers are, generally, hypersensitive to urban legends and even random tidbits that sound like they could be scientifically plausible. Maybe they should chill out.
Posted in link out, medicine, musings | 1 Comment »
March 12th, 2009 ecoli
I’m taking my first mathbio class this semester and I would like to share with you all the insights I’ve learned so far.
Most biological processes are 1st order dynamic systems. Meaning that, unlike many physical phenomena, the ‘momentum’ of a system has no affect on the trajectory. The only state that plays a role on the current state is the one directly preceding it.
Consider 2 changing populations with the same birth rate and no natural deaths. Lets say one starts at a 10 individuals and the other starts at 15. In the next generation, both populations double; 20 and 30. In population two, I now remove 10 individuals and allow the populations to double again. Both populations will end up with 40 individuals. Even though the second population started out with more, the only state that matters is the one directly preceding it.
Lets consider a linear, 1st order, system with two variables;
dx/dt = ax + by and dy/dt = cx/dy
What are some properties of this system (that we can extend to linear dynamic systems in general)?
1) at x = y = 0, the velocities are zero
2) If velocity at (x,y) is (Vx,Vy)
AND velocity at (x2,y2) is (Vx2,Vy2)
Then V(x1+x2,y1+y2) = (Vx1+Vx2,Vy1+Vy2)
3) If V @ (x,y) is (Vx,Vy)
then V @ (cx,cy) is (cVx,cVy)
Here is an example of the above. Consider:
dx/dt = -x & dy/dt = -y
In the graph we see a description of the differential equation system. Every arrow represents the velocity; direction and magnitude. All paths point towards the origin, and spot at the stationary point at (0,0).
Lets know consider a more complicated system with two variables.
dx/dt = x + y & dy/dt = -x + y
Again, at (x,y), V = 0. When y = 0, dx/dt = x and dy/dt = -x
In this scenario, we have a unique case at x = y; dx/dt = 2x and dy/dt = 0
Graphing this system of equations, we get something like:
In this system, we get what looks like an destabilizing stationary point at the origin, with a spiral shape pushing outwards.
If you were to imagine x and y as 2 populations over time, it would look as if x and y alternating maximums, but both maximums getting higher as time progresses:
While its doubtful that a population of two species look like this in nature, it helps demonstrate how changing populations over time can be modeled with differential equations. For example, if species y is a predator of species x and species x has ample resources to grow, a growth pattern like this could occur, as blooms in one species causes a bloom in the other, and species x is able to take advantage of crashing y populations, and ample other resources to rebuild its own numbers even greater than before.
I continue this series next time with more modeling of populations.
Posted in ecology, mathematics, medicine, musings | No Comments »
December 8th, 2008 ecoli
I couldn’t believe this story. Apparently, when smoked, the drugs are hallucinogenic. The problem is, of course, that there’s a limited resource of these drugs for the people that need them, but like any drug market, targeting abusers is more lucrative. HIV+ and health workers are the main suppliers to users in South Africa, which are mostly teens or high school age (15-21).
Posted in link out, medicine, news | 1 Comment »
August 29th, 2008 ecoli
These anti-vaccination people are getting ridiculous.
Posted in link out, medicine | No Comments »
August 8th, 2008 ecoli
Last night I was cutting up some of my homegrown Serrano chilies. I made a pretty good salsa with them (thanks to iNow for the recipe). However, I wasn’t prepared for the extreme heat of the peppers. I bit into one and my mouth almost literally caught on fire. I ignored the pain though and finished the salsa. About an hour later my hand started to burn and no amount of soap and water would significantly reduce the pain. As of right now, I’m still feeling it.
Being the naturally curious person, I wanted to find out more about why my hand felt like it was being knawed on by a million angry Gremlins.
Enter Capsaicins, the active ingrediant of the spicy heat of chilis:
Its a hydrophobic compound (which would explain why the water didn’t help) colorless and odorless but certainly not tasteless. It’s also an irritant for all mammals. Capsaicin is the most abundant of the capsaicinoid molecules found in chili peppers. The structure was first defined in 1919 by E. K. Nelson.
The capsaicins are found most abundantly in the placental tissue of the fruit. That is mainly the inner membranes and the white tissue holding the seeds, known as the pith, but not actually in the seeds themselves and in small amounts in the outer skin. Birds, which lack capsaicin receptors eat chilies and distribute their seeds after they pass safely through their digestive tracts.
In diluted form, the capsaicins are great for food, but can cause burning sensations when exposed in high concentrations to mucus membranes and skin, as I have discovered. The Scoville scale is a relative measure of how hot a pepper is, on the basis of perception. To demonstrate the scale, a bell pepper would get a zero rating, jalapenos are 2500-8000 (I assume non-pickled). My serranos would be rated around 10000 to 23000 and habeneros are 100000 to 350000. The Dorset Naga (yes grown in Dorset, England) tops the scales at 876,000 to 970,000. Nothing beats pure capsaicin, however, which weighs in at a hefty 15000000 on the Scoville scale.
So why do these capsaicins hurt so much? Its because they interact with sensory neurons. Capsaicins bind to vanilloid receptor subtype 1, an ion channel receptor which can also, incidently be stimulated by heat and abrasions. When opened, the channels allow calcium cations to pass through, depolarizing the cell membrane potential. From here, the electrical signal propogates down the neuron and is percieved ultimately in the brain.
So the reason why chilies make you feel like your toungue or hands are on fire, is because that’s exactly how your brain intepretes the neuronal signals. Of course, you know that there’s no actual heat present but, in this case perception is reality. Its nice to know that, while it may feel like you tounge is going to fall off, the capsaicins probably won’t cause real physical damage. However, it is an irritant, so injesting a large amount can be reasonto call the poison control center.
On the plus side, capsaicinoids have been useful in medicine, from treating topical pain in neuropathy to treating cancers and diabetes. Capsaicins can be a part of a healthy diet, as shown in epidemiological studies. Regions, such as Thailand, which use a healthy amount of chilies in their cooking have lower incidence of GI cancers. Capsaicins have been shown to promote apoptosis in lung cancer cells. New research also suggests that capsaicins could help reduce drug dependency.
So chilies taste good and are good for you, as long as you don’t over-ingest.
I can’t wait to go home and try my hot salsa.
Posted in biochemistry, medicine, neurobiology | 10 Comments »
August 7th, 2008 ecoli
This story has been big in the news lately. As you probably have already heard, the person who sent anthrax spores (Bacillus anthracis) through the mail has commited suicide. The culprit is army scientist Bruce Ivins.
Ivins worked with Anthrax in order to develop a vaccine, so one might think this is hypocritical to his work. However, current investigations lead us to beleive that Ivins was psychologically disturbed. Prosecuters speculate that Ivins was hoping to incense the public awareness of anthrax and hopefully get more funding. I guess scientists will go a long way to get research grants these days, but this is a new low.
My concern is how this event will ultimately change things for microbiologists and infectious disease researchers (a community I consider myself a part of). My lab doesn’t have anthrax, but we do have plenty of other deadly infectious diseases like Francisella tulerensis (tularemia), Yersinia pestis (bubonic plauge) and Borellia (Lyme’s disease).
Will researchers now have to get psych evals before we’re allowed to work with pathogens? Are intitutions going to tighten security, make us take even more safety classes, hire guards to check bags and not let us work alone? I hate to be the one to point this out, but it wouldn’t be exactly difficult to take pathogens out of the lab and even undergrads are given keys to the labs.
I have to sacrifice ease of access for security, but maybe the risks aren’t worth it? It just takes one incident to ruin it for the rest of us.
Perhaps (and hopefully) I’m wrong, and this will blow over as a unique incident, but it wouldn’t surprise me if universities, national and armed forces labs will at least start to discuss greater security measures.
Posted in medicine, microbiology, musings, news | 2 Comments »
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