Which Came First – The Chicken or the Egg?

One of the great things about having children is it reacquaints you with things you have not thought about for a long time. The old Chicken or the Egg paradox is one of those classic brain teasers that children of a certain age love. It is a really good one since the answer depends on how you parse the question. I thought I would list all the different answers my children and I could come up with.

Evolution 1 – Chicken

The first Chicken had to have hatched from an egg laid by a proto-chicken (i.e. a bird that was very similar to a chicken, but not actually a chicken). This means that the Chicken came before the first chicken Egg since only a chicken can lay a chicken egg.

Evolution 2 – Egg

If we consider that a chicken egg is an Egg that a Chicken hatches from then the Egg must comes first. It might have been laid by a Proto-Chicken, but out of this Egg hatched a Chicken.

Evolution 3 – Egg

The Egg is a much older than Chickens. What we now recognise as Eggs first appeared at least 300 million years ago. This was long before the first Chicken which is a domesticated version of the Indian Red Jungle Fowl from sometime in the last 10,000 years.

Evolution 4 – Unanswerable

Given that the definition of what separates a Chicken from a Proto-Chicken is undefined, it is not possible even in theory to say when the first Chicken hatched even if we had access to a time machine. If we can’t know when the first Chicken hatched we can’t answer the question.

Biblical – Chicken

According to Genesis 1 God created all the animals on Day 5 therefore the Chicken was created before the first Egg. It is an open question if the first Chickens were created with full formed eggs inside them and so if the first Egg was laid on Day 5 or not.

Word Order – Chicken

In the question “Which came first the Chicken or the Egg?”, the word Chicken precedes the word Egg.

Word Origin – Egg

The word Egg comes from Old Norse and ultimately back to the Proto-Germanic and before that Proto-Indo-European. It is a much older word than Chicken which is an Old English word of unknown origin.

English Language – Chicken

The original word for Egg in Old English was Ey and only in the development of Middle English did the Norse word egg become the common term. The word Chicken is from Old English and so it appeared first in the English language.

Dictionary – Chicken

In the English Dictionary the letter C comes before the letter E hence Chicken is first. The same applies to Encyclopaedias, although of course no child of today knows what an Encyclopaedia is.

Wikipedia – Chicken

The first entry for Egg was in 2005 while the first entry for Chicken was in 2004. Who would have guessed?

Finish Line – Chicken

In a race a Chicken will always beat an Egg to the finish line.

Drop Test – Egg

Chickens can fly so if you drop an Chicken and Egg off a barn roof together the Egg will hit the ground first. Chickens are surprising good flyers once they are allowed out to roam around for a few months.

There must be more!

Carnot Efficient Dyson Spheres are Undetectable by Infrared Surveys


An interesting series papers were published in The Astrophysical Journal in 2014 by J. T. Wright and colleagues who used data from the WISE and Spitzer wide-field infrared astronomical survey data sets to try to detect Dyson spheres [1-3]. While very thought provoking, the entire premise of their study rested on the assumption that the Dyson spheres created by advanced civilisations will radiate waste heat around 290K [2:2.6.4]. This assumption allowed them to hypothesise that Dyson spheres radiating waste heat at this temperature would show up as very bright infrared sources well above the 15-50K background emission from interstellar gas and dust clouds [2:2.6.4].

Wright et al. provided no detailed reason for assuming this waste heat value other than the Carnot efficiency of a Dyson sphere around a sun-like star is 0.95 at 290K [2:2.6.3]. They felt that this was a “reasonable” value to use, since in their opinion, it balanced the materials required to build a Dyson sphere with the overall Carnot efficiency [2:2.6.4]. An important question that needs to be considered is would any advanced civilisation capable of constructing Dyson spheres throwaway 5% of the potential energy available if this waste could be avoided? If we assume they could build more efficient Dyson spheres, would it be possible for us to detect them in the infrared spectrum above the background noise?

The Carnot efficiency of a Dyson sphere is determined by the Carnot equation η = 1 − Tw / T where T is the temperature of the star (5800K for a star like our sun) and Tw is the temperature of the waste energy emitted by the sphere [2:2.6.3]. To achieve a 95% Carnot efficiency around sun-like star a Dyson sphere needs to have a radius approximately that of Earth’s orbit (i.e. 1 AU) [2:2.6.3].

As the spheres diameter grows larger, the waste energy temperature becomes lower and the efficiency higher. For example, to achieve a Carnot efficiency of 99%, the Tw would need to be ~58K assuming a sun-like star. For a Dyson sphere to radiate at this temperature it would need to have a surface area 625 times greater than one that radiates at 290K (see equation 12 of [2]). This efficiency corresponds to a sphere with a radius of ~25 AU around sun-like stars.

For reasons unknown, Wright et al. decided to use a Carnot efficiency of 99.5% (with a corresponding Tw of 29K) in their counter example as to why 95% was a reasonable efficiency for any Dyson sphere building civilisation to use. They calculated that the sphere surface area to achieve this Carnot efficiency would need to have a surface area 10,000 times larger (100AU radius), but assumed that a Dyson sphere of this size would be impractical and hence only spheres with an efficiency of 0.95 would be built.

This is an unusual assumption to make since it means any advanced civilisation capable of building a Dyson sphere would have to waste 5% of the potential energy available. A 0.99 or better Carnot efficient sphere could be built using only a small fraction of the material resources available within our solar system [2]. If you are civilisation able to build a Dyson sphere the size of Earth’s orbit, then you would be able to build one larger and much more efficient using a relatively small increase in resources and time.

The consequences of this 0.95 efficiency choice is not minor. If Wright et al. had assumed Dyson spheres are 0.99 (or better) Carnot efficient then their emission spectra would not be detectable above the background infrared emissions of interstellar gas and dust – put simply, the emission signal from efficient Dyson spheres will be swamped by infrared noise in any wide-field infrared surveys.

Unfortunately this means that all we can conclude from Wright et al. study is that there are few (or no) Dyson spheres built with a 0.95 (or less) Carnot efficiency. If Dyson spheres do exist, and they are efficient (which we should expect of any advanced civilisation capable of building such spheres), we won’t be able to spot them via infrared astronomical surveys. The good news there is a different approach for finding efficient Dyson spheres, but that is another post.



2. Wright, J. T., Griffith, R. L.,  Sigurðsson, S., Povich, M. S., Mullan, B. (2014). THE Gˆ INFRARED SEARCH FOR EXTRATERRESTRIAL CIVILIZATIONS WITH LARGE ENERGY SUPPLIES. II. FRAMEWORK, STRATEGY, AND FIRST RESULT. The Astrophysical Journal: 792:27.

3. Griffith, R. L., Wright, J. T., Maldonado, J., Povich, M. S., Sigurdsson, S., Mullan, B. (2014). THE Ĝ INFRARED SEARCH FOR EXTRATERRESTRIAL CIVILIZATIONS WITH LARGE ENERGY SUPPLIES. III. THE REDDEST EXTENDED SOURCES IN WISEThe Astrophysical Journal: 792:28.

Preventing Global Climate Collapse

With the 2015 Paris Climate Agreement finished there has been a bit of discussion on Hacker News about how effective it will be in practice. I have my doubts that it will amount to much effective action, but it did remind me about the talk I gave in 2007 on how we could solve the problem of anthropic climate change via some clever financial engineering.

My basic idea was we shift the cost of stopping greenhouse gas (GHG) emissions onto the people who will really benefit (future generations) by issuing sovereign long term zero coupon bonds. The money from these bonds would be used to buy and shut down GHG emitting assets (oil, gas, coal) and build non-emitting alternatives (wind, solar, etc).

Combining this idea with some simple game theory, we can issuing these bonds today without requiring all countries to agree at once. The basic idea is that we put off allocating costs until when the bonds are due (zero coupon bonds don’t pay annual interest) and that they are ultimately allocated on the basis of the size of the economies at the time the bonds are due (50+ years) along with a discount for a country joining early. This avoids all the problems in deciding who should pay what share today.

If anyone is interested I have attached the slides from this talk. Some of the modelling and facts are a little out of date, but the basic framework is still valid. The major changes are the cost of GHG abatement has come down as wind and solar have got cheaper, and also long term interest rates are much lower than they were in 2007. Both these changes mean that it would cost far less than I estimated back in 2007. Now if we would only do something to solve this problem, not just sign agreements that have zero enforcement.

Preventing Global Climate Collapse Slides 2007

Ebola: What is happening?

As anyone alive in 2014 will remember Ebola was out of control and 2015 looked to be a horror with millions of deaths. Ebola then dropped out of the news and most people living far away from west Africa lost all interest. Unfortunately Ebola has not gone away and it still presents a risk for us all. So what is happening?

The new case numbers have stopped going down
At its worst Ebola was infecting a thousand people a week. We are now down to a new case number in the dozens (that we know of), but they do not seem to be getting any lower and these cases are occurring in locations that are very hard to get to (especially in the rainy season). As I mentioned last year one of my fears was if we didn’t put in a major effort into containing Ebola that it might become endemic in west Africa. It is looking more likely that Ebola will become another permanent member of the human disease pantheon rather than an episodic zoonosis.

Ebola did not become adapted to humans – yet
This was a very good outcome, but we still don’t know how difficult it is for Ebola to adapt to humans. Letting Ebola continue to spread (even at a low level) risks letting Ebola become better adapted to us. HIV is a good example to compare with Ebola. HIV was originally a zoonosis that did not infect humans very well. It took decades for HIV to become well adapted to infecting us. At the time HIV was going through this “infectiviness transition” (the 1920s to 1950s) we knew nothing about it so we can be excused for not doing anything, but this is not something we can say about Ebola.

The bottom line is that it is not a good idea to allow Ebola to continue to spread – each new case is potentially the first case of a new, more contagious Ebola.

So what should we be doing?
We really need to wipe out Ebola. This is not going to be easy especially now the rest of the world has lost interest. I still think this needs a military-like response, but it might be possible to use other approaches. What we don’t want to do is let Ebola fester away in west Africa for a few years only to be later surprised when a new, highly contagious strain pops up “unexpectedly” and spreads like a firestorm. We need to get the new case number to zero and the sooner the better. Time to get serious.

Why do we need to do anything about Ebola?

Figure 1. The Ebola virus (source CDC).

This is a good question. The current outbreak Ebola is happening in a part of the world (west Africa) where death is unfortunately all too common and where diseases like Malaria or HIV are killing many more people. Why should we care more about Ebola than HIV? Wouldn’t the resources required to stop Ebola be better spent controlling mosquitos (Malaria), or providing antiretroviral drugs to HIV patients? While I think these diseases are very important, and I wish the world did put more money into all infectious diseases, Ebola is different.


Ebola is spreading at a very rapid rate with the new case numbers doubling every 20 days or so. Diseases like Malaria and HIV are not spreading at anywhere near this rate, and while very serious, are not a threat that must be stopped today. The speed at which Ebola is spreading gives us very little time to develop control measures — we just don’t have the time to develop new drugs or vaccines (they are needed). Any delay makes the problem much, much bigger. Ebola is a problem that you can’t put off for tomorrow.

Ebola is not (yet) a human disease

This is a really important difference and one we should be most concerned about. Diseases like Malaria and HIV are human diseases, while Ebola is still a zoonotic disease caused by a virus picked up from an animal. Human diseases are adapted to infecting humans and being passed efficiently from person to person. How efficient a disease is passed from person to person is described by scientists using the term R0. This term tells you how many new people a person infected with the disease will on average infect. For example, a human disease like Polio has a R0 of between 5 and 7 (i.e. each person that gets infected with Polio will infect between 5 and 7 new people in an unvaccinated population). The R0 for Ebola in this outbreak is unknown (it ranges between under 1 to over 20 depending on the conditions), but the best estimate across the region is it is in the range of 1.3 to 1.8. This is quite low for an human disease and reflects that Ebola is not very good at being passed from person to person. This is not surprising when you remember that Ebola is a virus that normally infects flying foxes (fruit bats).

The major reason Ebola is not good at getting passed from person to person is that it kills you so quickly. Once you have symptoms you are normally dead (or hopefully on the way to recovery) within 7 to 10 days and before you have symptoms you are normally not infectious. This leaves very little time for Ebola to infect the next person, in fact Ebola is about as quick at killing humans as any disease can be and still be able to spread. If Ebola killed people any quicker (say within 3 days) then its R0 would be below 1 and the virus would have died out in humans on its own and never become a problem.

The fact that Ebola is infecting and killing thousands of people despite not being very good at it is worrying. Each person that gets infected produces hundreds of trillion of new viral particles. Many of these viral particles will have mutations (mistakes) in their genome (Ebola has a genome made up of RNA not DNA like in our own genome). Almost all of these mutated viruses are losers in the sense that the changes don’t improve Ebola’s ability to spread in humans, but just like with a lottery, the more tickets you buy the greater the chance you have of winning. By letting this outbreak run wild we are effectively buying trillions of tickets in a lottery we do not want to win — the human adapted Ebola lottery. Each person infected is making it a little more likely that a new mutant Ebola strain will arise with a much higher R0.

How would a such a mutated Ebola viral strain act? This is hard to say as we don’t know how well adapted Ebola can become to humans (we are in a way running a massive uncontrolled natural experiment to see how well adapted Ebola can become to infecting humans), but do we really want to find the answer to this question? Would it be wise to let a new strain arise that say took a month to kill you (thus allowing you to infect many more people), or one where you are infectious for a couple of weeks before the normal deadly symptoms arise? If such a strain arose then all our plans for containment of Ebola in western countries would be worthless.

We know how to stop Ebola

Unlike most human disease we actually know how to stop Ebola. All we need to do is get 70% of the infected people into simple treatment facilities where they can be cared for and where they can stop infecting new people. We have done this dozen of times with previous Ebola outbreaks and it has always worked. If we do this now we won’t have to worry about Ebola as future problem beyond being vigilant if any new zoonotic outbreaks occur. If we don’t stop this outbreak then we risk letting Ebola becoming entrenched in the human population like HIV or Polio. It is rare to have the ability to stop a new disease before it gets too big to control – let’s not let this opportunity go to waste.


One area that has received relatively little attention is the economics of Ebola. Even if the case numbers stay relatively low (say under 100,000), Ebola has the ability to cause major economic damage. As we have seen in recent weeks in the USA and other western countries, even a single imported case can cause mass concern (hysteria) leading to counterproductive proposals like travel bans and stopping flights. There is a real risk that politicians will overreact to the fears of an ill informed public and introduce policies that will disrupt international trade. The world economy is very weak; Europe is in or near to recession, China’s growth is slowing, Japan’s economy is running out of steam on the back of large VAT increases, and the resource-rich countries like Australia are slowing as commodity prices fall. With global interest rates at or near zero levels there is little that the world’s central banks can do to protect the world economy from even a small slow down in trade. With a fragile world economy we don’t want to be taking risks allowing anything that could derail growth and trade to run wild. Time to get serious.

Why do we need to go to full-scale military mobilisation to stop Ebola?

I posted last week that we need to move to full-scale military mobilisation if we are going to stop the current Ebola outbreak. After having some discussions about this on HN I thought that I should explain in more detail why we need to use the military and why we need full-scale mobilisation.

Scale of Problem

The problem is far beyond what any non-military organisation can deal with. This recent post from Les Roberts who is leading the WHO response in Freetown, Sierra Leone explains the scale of the problem.

The prediction landscape is looking bad. The official numbers reported are laboratory confirmed cases. Typically, we think people need 7-10ish days to become symptomatic. Typically people have symptoms for 7 days before they get into a health facility. A month ago, it was one day, now it typically takes 4 days from when a patient is sampled to when the patient is told the result of their test (and lots get lost and mislabeled….). Thus, the numbers that you hear about new cases today reflect the transmission dynamics from over 2 weeks ago…..and we thought the doubling time of the outbreak was 30 days, it seems to be less than that here. We knew the ~350 confirmed cases last week were an undercount….we now think there are 7-900 in reality. The need for hospital beds is climbing more than the ability to get them up and running. There might be 200ish ebola treatment beds now countrywide. There are perhaps 600 more in “holding areas.” We have schemes to get 500 or 600 ebola treatment beds up and running over the next 8 weeks. As Foreign Medical Team Coordinator, helping to get these beds up and supported is one of my primary tasks. If there are really 3000 cases this month, and 6000 next month…with all going perfectly on the treatment bed establishment side, we will have 30% of the beds we need next month, slightly worse than the situation now.

Need for effective quarantine

If we are going to get on top of the outbreak we need effective quarantine in the affected areas. Given the geographical scale of the outbreak, the poor infrastructure, and the limited local policing and military forces available, we need to bring in a lot of troops to do this. We also need to provide protection for the healthcare personnel and assist them in getting the sick out of homes and into treatment facilities. Only the military can provide this support.

Need for large numbers of healthcare personnel

We need thousands of doctors and nurses to run the treatment facilities. While we may get enough volunteers, the required numbers could soon exceed the number of volunteers we can recruit. If we run out of volunteers we would need to conscript the needed personnel and doing this would be impossible unless full-scale mobilisation had been authorised.

Toxic politics

Only full-scale mobilisation is going to short-circuit the political games being played. We have seen how hard politically it has been to get even a token number of USA troops deployed to west Africa. To send 40,000 or 80,000 troops and the associated healthcare personnel would be impossible in the current political climate. The only way to get the needed resources on the ground would be to effectively declare Ebola an international emergency and use the war powers available to Obama to do what needs to be done.

My fear is that we are not going to do this until the problem gets so huge that it will be beyond the world’s military to handle. The problem is doubling in size every 20 − 30 days, so each month of delay is making the problem more than twice as big. This is all without considering the risk of an Ebola strain arising that it is more infectious. Time to get serious.

Ebola: What needs to be done right now

I am a scientist with a background in Microbiology and Virology and what is happening (or more importantly what is not happening) with the current Ebola outbreak is very worrying. Rather than just scare my family I thought I should do a write up about what needs to be done.

Figure 1. Scale of the Ebola outbreak October 2014 (source WHO).

Where are we right now?

Ebola is completely out of control and the case numbers are doubling every 20 days or so. It does not look like Ebola had changed (it certainly could), it has just overwhelmed the containment systems we had in place in west Africa. The hospitals in the affected areas have reached (exceed) capacity and are not able to take in any new patients so the virus is running wild (this point seems to have been reached around August). A consequence of this is we really have a very poor idea of the number of cases since no-one is recording the cases that don’t make it to hospital.

What is going to happen?

Ebola is actually a very well studied virus from an epidemiological perspective so we can model its spread quite accurately. Here is what is going to happen according to the CDC.


Figure 2. Estimated impact of delaying intervention* on daily number of Ebola cases, with and without correction for underreporting† — EbolaResponse modeling tool, Liberia, 2014–2015 (source CDC).

* Intervention: Starting on September 23, 2014 (day 181 in model), and for the next 30 days, the percentage of all patients in Ebola treatment units was increased from 10% to 13%. This percentage was again increased on October 23, 2014 (day 211 in model) to 25%, on November 22, 2014 (day 241 in model) to 40%, and finally on December 22, 2014 (day 271 in model) to 70%. Day 1 in model is March 3, 2014. The impact of a delay of starting the increase in interventions was then estimated by twice repeating the above scenario but setting the start day on either October 23, 2014, or November 22, 2014.
† Corrected for potential underreporting by multiplying reported cases by a factor of 2.5 (Table 4).
§ New Ebola patients at peak of each start date. (Note that when the intervention is started on November 22, 2014, the peak is not reached by January 20, 2014, which is the last date included in the model.)

The only thing missing from this modelling is the “do nothing” option since the CDC has assumed that we will start doing something by November 22nd (unlikely). They have also been too scared to model past January 2015.

This modelling also assumes that the virus does not become better adapted to spread in humans which could, and may even be likely, to happen. The most probable adaption would not be for Ebola to become airborne (this is only slightly less likely than pigs becoming airborne), but for the virus to slow down in the speed in which it kills people so they stay infectious for a longer period of time. A strain could arise that takes a month to kill you (rather than a week) and where you are asymptomatic, but infectious, for a couple of weeks. Such a strain would allow each patient to infect many more people before they died or recovered. One of the reasons that Ebola has not caused major outbreaks in the past is that it kills so rapidly that there is little time for each patient to infect new people. The selection pressure on Ebola to slow the speed in which it kills is extremely strong and the more people infected the more likely it becomes that such a mutation will occur.

Why did this Ebola outbreak get so bad?

This is a good question as it is not the first Ebola outbreak. The best explanation I have seen is from the discoverer of Ebola, Professor Piot, as quoted in De Spiegel.

SPIEGEL: Why did WHO react so late?

Piot: On the one hand, it was because their African regional office isn’t staffed with the most capable people but with political appointees. And the headquarters in Geneva suffered large budget cuts that had been agreed to by member states. The department for hemorrhagic fever and the one responsible for the management of epidemic emergencies were hit hard. But since August, WHO has regained a leadership role.

What do we need to do to stop Ebola?

We need to get the R0 below 1. This means each infected person needs to infects less than one new person. Right now the R0 is somewhere between 2 and 10 (i.e. each infected person is infecting between 2 to 10 new people). To get the R0 of Ebola below 1 we need to move at least 70% of infected people into properly functioning infection control hospitals. Sounds easy doesn’t it?

How do we actually do this?

This outbreak is now beyond the ability of the governments in the affected areas, the WHO, or any NGO to bring under control (the head of MSF has stated that the outbreak is now beyond their ability to deal with). There is only one option left which is full-scale military mobilisation. In practicable terms this is what needs to happen:

  • The UN Security Council needs to authorise the use of all available resources to control and contain the outbreak in the affected countries and surrounding regions including the use of international military force. This needs to be done as soon as possible (days not weeks).
  • Those countries with the ability to do this (the USA mostly) need to move to full-scale military mobilisation (i.e. war level)*. This may require conscription of the required healthcare workers, but if we are lucky and act soon we might be able to get by with just volunteers.
  • Start an outside-in Ebola containment/infection control process in the region. This will require putting large numbers of troops and medical personnel on the ground in the surrounding countries and then moving into the worst affected areas as more hospitalisation capacity is brought online. The key is to fight Ebola where it can be controlled so that it does not spread further and not waste our resources fighting it in those areas where we can’t get the R0 below 1 (i.e. where we can’t achieve the required 70% hospitalisation rate).

*Why do we need mobilisation? In theory we don’t, but politics in the USA is so toxic that unless this is treated as war it won’t be possible to get the required resource on the ground quickly enough. An example of this is the 3000 troops announced a couple of weeks back that were going to be sent to Liberia to help have still not left as they are being held up by congress as politics is played.

What do I think will actually happen?

A lot of dithering and token efforts from the UN and the rest of the world until January 2015 when wholesale panic sets in and we then move to full-scale mobilisation. If we are lucky the virus won’t have mutated and will only destroy west Africa. By the end of 2015 a 100 million people could be dead and the world in a massive recession as international trade grinds to a halt. Of course I could be wrong (I certainly hope I am), but based on what I know and what I see happening (or more importantly not happening) I am not that hopeful. Time to get serious.

Install R on CentOS 5 x64 using yum

I recently had the fun of installing R on my development box. While you can install from source I wanted to be able to install using yum. R is not in the standard packages, but it is in the epel repository (Extra Packages for Enterprise Linux 5 – x86_64).

Steps for Installing R
1. Make sure that you have epel in your yum repositories (use yum listrepo to check). If not add epel to your yum repos (see here for instructions how to do this).
2. Install R and dependencies using yum install R-core R-2*
3. Enter R (just type R) and update all the default package using update.packages(). You will need to choose the nearest mirror to you.
4. Install the packages you need using install.packages(“package_name”, dependencies = TRUE)
5. Quit R using q()

Hope this saves someone a little time.

If you are behind a proxy server then use the following (change for your proxy setting) after starting R
You can check if correct by
then update by