What was it, roughly, that we were thinking there, if anything? Part two.

So, there was a high school class reunion a few months back, and it’s World Series time again, so now seems a good time for an overdue, second episode of our series of the above title. In episode one, I explored an incident involving sub-optimal decision making in high school so I think I’ll just continue on that theme here.

I saw a number of old classmates, and teammates, at the reunion. I think class reunions are great. They can cause one to reflect on really important topics, such as the passage of time, or the nature of life’s changes. Or to even deeper things. Explosives for example. Just what “loud” really entails. The nature of stupidity.

It seems that I had become aware that personal fireworks were legal in the next county, and had thus traveled the 40 miles to obtain a few dozen “M-80” fireworks, ostensibly for use during the Fourth of July. It also seems that sometime later, my friend Steve and I found ourselves parked in front of our friend Doug Brown’s house after dark, with said bag of M-80s and a lighter. Now, an M-80, we’d been told, contained the equivalent gunpowder of a quarter stick of dynamite, which I thought was pretty impressive but did no actual testing of. If one of these things goes off on, say, someone’s front porch, it would not typically go unnoticed, and that concept did seem, to us, worthy of some testing at that particular time.

It additionally seems that I was the driver and Doug’s house was off to our left. The plan, which I think we put a solid 30 seconds of thought into, was that we would launch one of these onto Doug’s porch–about maybe 75 ft away–while seated in the vehicle, so as to effect a prompt getaway. We came up with a fair and efficient division of labor in which Steve would light the fuse and hand the thing to me–I would then fire it toward the porch and immediately hit the gas, making ourselves rapidly scarce. It was a great plan as far as I was concerned: all I had to do was throw and floor it, whereas Steve had the equivalent of six to eight sticks of dynamite in a bag on his lap, with an open flame in his hand. This struck me as equitable, given that I was providing the vehicle and the right arm.

So…what’s the baseball connection here, you may wonder. Well, I played shortstop in high school, whereas Steve didn’t, and so it was logical that I should do whatever throwing was involved. Shortstop is a fun position, because you get to sprint to chase down ground balls, and then watch the first baseman sprint to chase down the throw you just sailed some distance beyond him. Now, 70-80 feet is a lot shorter than a typical throw from shortstop to first base…but an M-80 is also a lot lighter than a baseball. So I knew I should put some mustard on it to insure getting it at least somewhere near the porch. Being quite experienced at firing balls into the adjacent woods from deep short, I wasn’t too worried about it. If the M-80 banged off the front of the house first or whatever, no big deal, I mean assuming nobody opened the front door at the wrong instant.

Now may be a good time to remind ourselves of the importance of taking all potentially relevant variables into consideration–apriori even–in events like these. And do we think enough about the tangible value of trial runs? Probably some room for improvement there too.

Anyway, Steve successfully got said firework lit without blowing us up, and the ensuing exchange to me was also flawless. With right arm extended and a good five seconds or so to work with, I eyed Doug’s porch and applied my best Nolan Ryan fastball to the explosive. Now, I think it’s fair to say that (1) the average person is just not that aware of exactly where one’s car door meets one’s car roof, (2) that I qualify as quite average in that context, and (3) that that specific location took on above average significance, in that particular situation. In short, when my hand was just about to send said explosive device on it’s planned trajectory, said hand was inadvertently applied, with considerable force, to said vehicular location, and separated from said device, thereby placing the latter on a trajectory not nearly as likely to achieve the original objective. This in turn would necessitate a rapid adjustment in plan and action, not to mention vocalization.

This is more or less a science blog, and I ask you, are many topics more fascinating, really, than the physics of acoustics under confinement? Maybe heredity–I find that interesting too. Also, involuntary reflexes, impromptu vocalizations: good stuff. How about hand-eye coordination under duress? Personal safety and survival? Blood?
Bodily dismemberment? All topics worthy of consideration when you get down to it. Let’s explore some of these for just a moment.

Acoustic physics, let’s take. As we know, Newton’s First Law of Loud, states “Any acoustically active device, placed under spatial confinement, will manifest even more of its acoustic characteristics, in fact quite a lot more than you’d think just from theory alone”. Take spatial relationships: just how much room for rapid bodily movement is there, really, in the front passenger seat of a typical car? How can humans maximize movement efficiency in response to active, explosive devices experiencing random trajectories?

Now back to our story. To cut to the chase, upon hand-car impact, our active device–the one under current discussion–experienced a rather sudden change of x coordinate velocity–one markedly away from Doug’s front porch, opposite that really, which is to say in the general direction of one Steve. More specifically, toward Steve’s male-specific, hereditarily significant anatomy. And there it landed, for a brief moment. Although entirely stunned, and with my hand feeling possibly broken, I was still able to collect myself, breathe a sigh of relief and comment on just how fortunate we were, really, that said M-80 had not taken an alternate trajectory and landed instead, in or near the bag of 30 or so other M-80s, within the confines of our vehicle, in which we too were present, due to our plan, in the street in front of our friend Doug Brown’s house. Steve also reflected for a bit on this fortunate state and concurred that such an outcome would have been potentially problematic on several counts, not the least of which was just how autopsies and identifications based on scattered body parts are conducted.

The preceding is not in fact what transpired at that moment.

Rather, Steve executed what I think to this day is the most rapid series of body movements I’ve ever seen from a human being, with the possible exception of the time I scrambled up and over a rock to find my neck about three feet directly in front of the head of a large rattlesnake. Conscious thought was not part of the process. M-80s had fuse times of roughly six to seven seconds, going strictly from memory. I’d guestimate that at this point, about four of those remained. As I recall it, there were, in order (1) an involuntary yell, (2) a ceiling-constrained jump upward, and (3) a failed attempt to flick the thing, by a backhand motion, away from where it resided. This process took maybe two seconds, maximum, and led to another entirely frantic attempt–panicked would work–which succeeded in flinging the thing down towards Steve’s feet. This, very fortunately, was not where the bag of other M-80s had been placed, and additionally, it’s one thing to have your feet blown off but quite another to have your evolutionary lineage ended.

Down there our device detonated, with a flash, maybe 1 to 1.5 seconds later.

What M-80 detonations lack in duration and beauty of light display they make up for in sheer decibels; they aren’t fireworks so much as small bombs. This was the most unbelievably loud thing I’d ever heard, and that includes seeing Ted Nugent in the old concrete and steel Toledo Sports Arena (also with Steve). It was concussive. Steve told me he basically could not hear for several days. The car was immediately filled with an acrid cloud of sulfurous smoke. My hand felt very possibly broken. I could neither hear nor see, and my first thought was “We gotta get out of here right NOW, before Doug comes out and sees this”. Or even worse, his dad, with a possible call to the police. But even in the best of circumstances, it’s not easy to go straight from Nolan Ryan to Mario Andretti, quickly. I could not see without sticking my head out the window, which I did until the breeze created cleared out the cab. I’m not sure that Steve knew exactly what had happened or even where he was, but didn’t have time to investigate. I was pretty sure he was alive and that would have to be good enough for the moment.

I think the evening’s festivities were concluded with this event, although I wouldn’t necessarily place money on that either. If Doug is reading, I’d like to formally apologize for the rubber patch laid in front of his house and any subsequent effect on property values that may have resulted.

Thanks for reading and please stay tuned for the next episode, in which we’ll explore how surprisingly inconvenient cul-de-sacs can be in certain circumstances, and/or other fascinating topics.

The devil’s real

The devil ain’t a legend; the devil’s real
In the empty way he touched me, where I hardly feel
In the empty hole inside me, the nothin’ that will drive me
Down into my grave: it does not heal
Nothing is a something, and it will suck you dry
Like the whisper you can hardly hear that tells you why

They told me “you ain’t got no problems, you’re self deceived;
These seeming contradictions, well they’re make-believe”
It was then that I decided that my life was being guided
By a second rate dependence on some first class thieves
They told me I was breakin’ through, but I was breakin’ down
And by the time I learned the difference they had long left town

You know they ain’t so malicious, they ain’t mean
They’re just vaguely well intentioned with no love I’ve seen
And its the emptiness that kills you, cold comfort that will fill you
With a sense of dread that maybe things are worse than they seem
They don’t tell you nothin’ you don’t already know
They just keep holding out a promise…but they don’t let go
You know they don’t let go

Well it was hard luck and trouble–bad times two
I know I had it comin’, but I got through
It was advice that you gave me, in a dream, that saved me
You said “get a new life contract that spells out your dues”
It took good will to find it, and a clear conscience to sign it
But now I dream about the good times and it all comes true
Yeah I dream about the good times and it all comes true

The Devil’s Real, Chris Smither

Ebola epidemic update

Today a new and more extensive WHO W. Africa ebola update was released, including data current as of Sept. 14, four days ago. I’ve therefore compiled new tables, and case and death rates. The new code and graphs are here, and the new data table is here. Liberia-specific graphs are here.

There’s been a slight drop in the transmission rate, based on these data. The daily rate is now estimated at about 1.038 (down from 1.043 a month ago). The 6-12 day rates, which correspond roughly with the estimate of R_zero, the per person rate of infection (depending on the mean infectiousness period, in days), range from 1.25 to 1.57. The midpoint value is 1.41. See here and here for my methodology.

It is almost certain that cases are going unreported however, and it could be many, I don’t know. These estimates are therefore underestimates of the true rate, and hence the severity of the outbreak. And this kind of thing is certainly tragic and not helping the situation.

Estimating the spread rate in the current ebola epidemic

I’ve now written several articles on the West African ebola outbreak (see e.g. here, here, here, and here). This time I want to get more analytical, by describing how I estimated the ebola basic reproduction rate Ro (“R zero”), i.e. the rate of infection spread. Almost certainly, various people are making these estimates, but I’ve not seen any yet, including at the WHO and CDC websites or the few articles that have come out to date.

Some background first. Ro is a fundamental parameter in epidemiology, conceptually similar to r, the “intrinsic rate of increase”, in population biology. In epidemiology, it’s defined as the (mean) number of secondary disease cases arising from some primary case. When an individual gets infected, he or she is a secondary case relative to the primary case that infected him or her, and in turn becomes a primary case capable of spreading the disease to others. It’s a lineage in that respect, and fractal. I’ll refer to it simply as R here.

The value of R depends strongly on the biology of the virus and the behavior of the infected. It is thus more context dependent than the r parameter of population biology, which is an idealized, or optimum, rate of population growth determined by intrinsic reproductive parameters (e.g. age to reproductive maturity, mean litter size, gestation time). Diseases which are highly contagious, such as measles, smallpox and the flu, have R values in the range of 3 to 8 or even much more, whereas those that require direct exchange of body fluids, like HIV, have much lower rates.

To slow an epidemic of any disease it is necessary to lower the value of R; to stop it completely, R must be brought to zero. Any value of R > 0.0 indicates a disease with at least some activity in the target population. When R = 1.0, there is a steady increase in the cumulative number of cases, but no change in the rate of infection (new cases per unit time): each infected person infects (on average) exactly 1.0 other person before either recovering or dying. Any R > 1.0 indicates a (necessarily exponential) increase in the infection rate, that is, the rate of new cases per unit time (not just the total number of cases), is increasing.

Continue reading

Liberian ebola rate jumps

Updated as of 09-18-2014 WHO report.

Many reports from on-the-ground workers with the WHO, Doctors Without Borders, state health and aid agencies, etc. have commented that the case and death rates in at least some locations have almost certainly been too low, because of a substantial number of people avoiding going to clinics and hospitals, out of fear primarily. This situation seems to be the worst in Liberia. See this article for example. Today’s WHO-released data from Liberia may be confirmation of this, many new cases and deaths being reported there from August 16-18. Such an explanation could be due to more intensive case tracking/finding. However, it is also possible that the epidemic is simply exploding there now, especially given that it is well established in the capitol of Monrovia. Or it could be due to some combination of the two.

In the graphs below I used a pretty stiff “span” parameter (span = 1.0) in the loess smoothings (dark black lines) of the WHO-reported raw data (thin line). This choice gives about 35 deaths/day in Liberia. If I use something more flexible, span = 0.5 for example, the estimated rates are higher, about 47/day. However, it’s best to go stiff (i.e. conservative) here, because clearly there are major variations due to data gathering and reporting timelines that have been causing large fluctuations in the numbers (discussed more here).  But there’s also clearly more than just that going on with this latest surge in numbers.

This situation is now extremely serious, if it wasn’t already. Note also that negative rates early on in the outbreak are presumably due to case retractions or re-classifications. Code generating data and graphs is here and data table itself is here.

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Ebola rates, updated

Latest data from the WHO on the W. Africa Ebola outbreak (report of 09-18-14; data therein as of 09-14-14). For data table go here, and for R code generating data and graphs go here.

Reporting issues are likely responsible for the large fluctuations in the raw data, hence the loess smoothing (dark line) for a better approximation of the true rates. See here for a more in depth discussion of this issue.
Ebola case recent rates 2q
Ebola death recent rates 2q

Ebola epidemiology data scraper

Note: The following post is current as of WHO report of 09-18-14, which includes data to 09-14-14. [I’ve altered this code a number of times because of the nearly constantly changing format and location of the WHO data.]

I wanted to find certain statistics for the West African Ebolavirus (EBV) outbreak from its inception, e.g. recent case and death rates. By “recent” I mean at WHO GAR reporting intervals, typically a few days. But the sites where I’d expect to find such (WHO, CDC etc) didn’t have them, at least in a synthesized form. So, I wrote an R script to scrape, compile, rearrange, and plot the data, for any country or all together, as taken from two sources. Starting with the WHO July 1 GAR report, tables of new and cumulative cases and deaths, categorized by degree of certainty, for each of the three countries in the outbreak, are given. Wikipedia has a less detailed table for all dates from March 25 on. I used it to obtain total cases and deaths up to July 1.

Below are graphs of the recent, per-day (1) case rates, and (2) death rates, from March 22. Each shows the raw data (thinner line), and a loess-fitted trend (thicker line). Note that reporting issues are partly, perhaps largely, responsible for extreme fluctuations in the raw data.

Ebola case recent rates 2q
Ebola death recent rates 2q

Continue reading

Ebola references (updated)

This is an abbreviated list of freely accessible, Ebola-related articles. Some are specific to the current outbreak, others are more general, some traditional science articles and others good online articles. [There are also a couple of useful links in the article below.] There will likely be a large number of articles emerging, potentially very large, given the nature of the situation.

1. Scientific literature and reports:
Atherstone et al., 2014. Ebola risk assessment in the pig value chain in Uganda (a good article, much more comprehensive than the title would indicate!)

Baize et al, 2014. Emergence of Zaire Ebola Virus Disease in Guinea-Preliminary Report

Bausch et al., 2014. Outbreak of Ebola Virus Disease in Guinea: Where Ecology Meets Economy.

CDC Mortality and Morbidity Weekly Reports, 2014. Ebola Viral Disease Outbreak — West Africa.

Dudas and Rambaugh, 2014. Phylogenetic Analysis of Guinea 2014 EBOV Ebolavirus Outbreak.

Feldman et al, 2003. Ebola virus: from discovery to vaccine.

Gatherer, 2014, (in press). The 2014 Ebola virus disease outbreak in west Africa

Legrand et al., E&I, 2007. Understanding the dynamics of Ebola epidemics.

Leroy et al., 2001. Early immune responses accompanying human asymptomatic Ebola infections

Muyembe et al., 2012. Ebola virus outbreaks in Africa: Past and present

Vanessa and Matthias, 2012. Infection Control During Filoviral Hemorrhagic Fever Outbreaks

2. Web pages:
WHO, 2014. Ebola virus disease, West Africa – update 10 July 2014

WHO, 2014. EBV FAQ

Laden, G., 2014. Ebola Outbreak in West Africa: Some basic information (Updated)

Black, 2014, on-site reporting (doctor with DWB, on scene in Sierra Leone), In the Shadow of Ebola and The First 24 Hour Shift

Poon, 2014, WUNC Radio. Ebola 101: The Facts Behind A Frightening Virus.

Ebola update

The West Africa Ebola epidemic is not waning. The latest (July 6) numbers from the WHO show that about 5.6% of the total cases (including probable and suspect cases), and 4.6% of the deaths, originated just in the four days from July 3 to July 6, inclusive. The minimum mortality rates are 350/626 (56%) for confirmed cases, and 543/894 (61%) when also including probable and suspect cases. The epidemic appears to be moving out of Guinea, and into Liberia and Sierra Leone, based on the recently reported cases. The WHO Ebola FAQ is here if you want to learn more about it, but on the outbreak itself there appears to be a serious dearth of reliable information.

  Country  Date   Type New* Confirmed Probable Suspect Total
1  Guinea 07_08  Cases    0       294       96      18   408
2 Liberia 07_08  Cases   16        63       30      38   131
3    S.L. 07_08  Cases   34       269       34       2   305
4   Total 07_08  Cases   50       626      160      58   844
5  Guinea 07_08 Deaths    2       195       96      16   307
6 Liberia 07_08 Deaths    9        41       28      15    84
7    S.L. 07_08 Deaths   14       114       11       2   127
8   Total 07_08 Deaths   25       350      135      33   518
#  *New cases (reported since 07_03) are neither classified nor included in Total

Updated values as of 7-10-14:

  Country  Date   Type New* Confirmed Probable Suspect Total
1  Guinea 07_10  Cases    1       296       96      17   409
2 Liberia 07_10  Cases   11        70       32      40   142
3    S.L. 07_10  Cases   32       298       34       5   337
4   Total 07_10  Cases   44       664      162      62   888
5  Guinea 07_10 Deaths    2       197       96      16   309
6 Liberia 07_10 Deaths    4        44       28      16    88
7    S.L. 07_10 Deaths   15       127       11       4   142
8   Total 07_10 Deaths   21       368      135      36   539
#   *New cases (reported since 07_08) are neither classified nor included in Total

1. New articles, both good, on Doctors Without Borders and The Economist web sites.

2. The Wikipedia page on the topic contains a summary table of the weekly course of reported cases and deaths since March.

The West Africa Ebola outbreak

A WHO-organized meeting on the current, West African Ebola outbreak is occurring today and tomorrow in Ghana. The outbreak began several months ago in Guinea, with a significant mortality event in mid-March, and now a significantly larger and more extensive second outbreak has occurred in May/June. According to CDC numbers, it has now officially become the worst outbreak, in terms of fatalities, in the ~50 year (known) history of the disease, with 441 dead. Ebola emerged without warning in Zaire in 1976, and the viral family it belongs to, the Filoviridae, was not even discovered until 1967 (see this interesting document). The WHO estimates the mortality at 291 confirmed and 467 probable. The cause of the difference in the two mortality estimates is not immediately clear to me. You can learn more about Ebola and Marburg, two of the hemorrhagic viruses, here. Here is a summary of how the WHO is handling the situation.

EVD-outbreak Source.

Ebola casesThe growth in Zaire Ebolavirus cases as of June 24, n = 607. LAB+: laboratory confirmed. Source.