Saturday 18 July 2009

Quantitative Intuition

To be good at quantification you need to develop an intuition about the relative magnitudes of the quantities you are interested in. This is highlighted nicely by this quote from William Ayrton

"One of the great difficulties experienced by people in mastering the quantitative science of electricity, arises from the fact that we do not number an electrical sense among our other senses, and hence we have no intuitive perception of electrical infant has distinct ideas about hot and cold, although it may not be able to put its ideas into words and yet many a student of electricity of mature years has but the haziest notion of the exact meaning of high and low potential, the electrical analogues of hot and cold."

William E. Ayrton, Practical Electricity, 1887, Preface.
Cited in The morals of measurement. Graeme Gooday. Cambridge University Press. 2004

Carlson Curve

I have written already about Moore's law, and its profound impact on society and science. However, there are other well known geometric progressions in technology, this paper is one example - Carlson, R. (2003). The Pace and Proliferation of Biological Technologies. In Biosecurity and Bioterrorism: Biodefense Strategy, Practice, and Science Volume 1 No. 3.


The development of powerful laboratory tools is enabling ever more sophisticated measurement of biology at the molecular level. Beyond its own experimental utility, every new measurement technique creates a new mode of interaction with biological systems. Moreover, new measurement techniques can swiftly become means to manipulate biological systems. Estimating the pace of improvement of representative technologies is one way to illustrate the rate at which our ability to interact with and manipulate biological systems is changing."

Here is Figure 1 from the paper.

FIG. 1. On this semi-log plot, DNA synthesis and sequencing productivity are both increasing at least as fast as Moore?s Law (upwards triangles). Each of the remaining points is the amount of DNA that can be processed by one person running multiple machines for one eight hour day, defined by the time required for preprocessing and sample handling on each instrument. Not included in these estimates is the time required for sequence analysis. For comparison, the approximate rate at which a single molecule of E. coli DNA Polymerase III replicates DNA is shown (dashed horizontal line), referenced to an eight-hour day.

Sample processing time and cycle time per run for instruments in production are based on the experience of the scientific staff of the Molecular Sciences Institute and on estimates provided by manufacturers. ABI synthesis and sequencing data and Intel transistor data courtesy of those corporations. Pyrosequencing data courtesy of Mostafa Ronaghi at the Stanford Genome Technology Center. GeneWriter data courtesy of Glen Evans, Egea Biosciences. Projections are based on instruments under development.

McLuhan on TV & Comics asVisual media

"From the three million dots per second on TV, the viewer is able to accept, in an iconic grasp, only a few dozen, seventy or so, from which to shape an image. This image thus made is as crude as that of the comics. It is for this reason that ... the comics provide a useful approach to understanding the TV image, for they offer very little visual information or connected detail."

Understanding Media: The Extensions of Man. New York: McGraw-Hill, 1964 (pg 150).

Wells & Bush on Information

Data Deluge speaks strongly to the dramatic technological changes of the past 20 years or so. But it is of course part of a longer trend over the past 100 years in which the idea that increases in material culture and technology were posing both opportunities and issues associated with a deluge of data and information.

For example, the British science fiction write H.G. Wells imagined in the late 1930’s what a 'World Brain’ would be like and what it would enable (Wells 1938). His idea was that in the future scholars would have access at their desks to the complete catalogue of the Worlds knowledge. Wells imagined that this would be enabled by photographic means - based on the idea of microfilm and microfiche. However, if one replaces talk of micro-fiche with digital data then we can see just how prescient Wells’ vision was;

”our contemporary encyclopedias are still in the coach-and-horse phase of development, rather than in the phase of the automobile and the aeroplane. These observers realize that the modern facilities of transport, radio, photographic reproduction and so forth are rendering practicable a much more fully succinct and accessible assembly of facts and ideas than was ever possible before.”

Wells was not alone, at the end of the second world war the US politician and thinker Vannevar
Bush wrote a piece for Atlantic Magazine in which he reflected on the enormous changes that science and technology had brought in (Bush 1945). He marveled at the fact that;

”There is a growing mountain of research. But there is increased evidence that we are being bogged down today as specialization extends. The investigator is staggered by the findings and conclusions of thousands of other workersconclusions which he cannot find time to grasp, much less to remember, as they appear . . . Professionally our methods of transmitting and reviewing the results of research are generations old and by now are totally inadequate for their purpose.”

These thinkers had enormous foresight. They had begun to observe a significant change in the volume of data and information arising in general, and in scientific and technical work in particular, and realised that there were real issues raised by the deluge of information.

How long is a Petabyte life?

I have been thinking about Petabytes and tryng to get some perspective on how much data that really is.

In digital data terms a petabyte is a lot of data. 1 PB = 1,000,000,000,000,000 B = 1015 byte. Assuming a byte is 8 bits then a petabyte is 8 x 1015 bits.

According to this paper, Google processes more than 20 Petabytes of data per day using its MapReduce program.

According to Kevin Kelly of the New York Times, this reference, "the entire works of humankind, from the beginning of recorded history, in all languages" would amount to 50 petabytes of data.

These are all difficult to understand as they are abstract. So I tried to find a way of understanding what a Petabyte is in human terms. Scientific researchers estimate that the human retina communicates with the brain at a rate of 10 million bits per second (Reference HERE) or 106 bits per second. This sounds pretty impressive. How long does it take a human eye-brain system to move a petabyte of data (assuming that you could keep your eyes permanently open so that you are getting your full 10 million bits per second).

By my calculations a year is 3.15 x 107 seconds. This means a total amount of data per year from retina to brain of 3.15 x 1013 bits. Dividing 8 x 1015 by 3.15 x 1013 we get 254 years. This is a long time to keep your eyes open!

If we take a normal human life to be the biblical standard of Psalms 90: The days of our years are threescore years and ten, then a normal human creates about 0.27 petabytes in their life.

So I will define a new unit, the PetaBlife, with a symbol which is the number of standard human lifetimes required for a human retina to make a PetaByte of data.

If we take Google seriously, then each year they are processing the equivalent of 7.3 x 103 ℘.


Thursday 16 July 2009

No evidence that prayer alleviates ill health

The following is NOT a hoax. It is the summary of a recently published Cochrane review of the evidence for or against the effects of intercessory prayer for the alleviation of ill health.

In fact this is a great example of an objective and balanced analysis of the evidence for the efficacy of a treatment. Full report HERE.

Intercessory prayer for the alleviation of ill health

Leanne Roberts1, Irshad Ahmed2, Steve Hall3, Andrew Davison4

1Hertford College, Oxford, UK. 2Psychiatry, Capital Region Mental Health Center, Hartford, Connecticut, USA. 3The Deanery, Southampton, UK. 4St Stephen's House, Oxford, UK

Contact address: Leanne Roberts, Hertford College, Catte Street, Oxford, OX1 3BW, UK. (Editorial group: Cochrane Schizophrenia Group.)

Cochrane Database of Systematic Reviews, Issue 3, 2009 (Status in this issue: Edited, commented)
Copyright © 2009 The Cochrane Collaboration. Published by John Wiley & Sons, Ltd.
DOI: 10.1002/14651858.CD000368.pub3
This version first published online: 15 April 2009 in Issue 2, 2009. Re-published online with edits: 8 July 2009 in Issue 3, 2009. Last assessed as up-to-date: 13 November 2008. (Help document - Dates and Statuses explained).

This record should be cited as: Roberts L, Ahmed I, Hall S, Davison A. Intercessory prayer for the alleviation of ill health. Cochrane Database of Systematic Reviews 2009, Issue 2. Art. No.: CD000368. DOI: 10.1002/14651858.CD000368.pub3.


Prayer is amongst the oldest and most widespread interventions used with the intention of alleviating illness and promoting good health. Given the significance of this response to illness for a large proportion of the world's population, there has been considerable interest in recent years in measuring the efficacy of intercessory prayer for the alleviation of ill health in a scientifically rigorous fashion. The question of whether this may contribute towards proving or disproving the existence of God is a philosophical question lying outside the scope of this review of the effects of prayer. This revised version of the review has been prepared in response to feedback and to reflect new methods in the conduct and presentation of Cochrane reviews.

To review the effects of intercessory prayer as an additional intervention for people with health problems already receiving routine health care.

Search strategy
We systematically searched ten relevant databases including MEDLINE and EMBASE (June 2007).

Selection criteria
We included any randomised trial comparing personal, focused, committed and organised intercessory prayer with those interceding holding some belief that they are praying to God or a god versus any other intervention. This prayer could be offered on behalf of anyone with health problems.

Data collection and analysis
We extracted data independently and analysed it on an intention to treat basis, where possible. We calculated, for binary data, the fixed-effect relative risk (RR), their 95% confidence intervals (CI), and the number needed to treat or harm (NNT or NNH).

Main results
Ten studies are included in this updated review (7646 patients). For the comparison of intercessory prayer plus standard care versus standard care alone, overall there was no clear effect of intercessory prayer on death, with the effect not reaching statistical significance and data being heterogeneous (6 RCTs, n=6784, random-effects RR 0.77 CI 0.51 to 1.16, I2 83%). For general clinical state there was also no significant difference between groups (5 RCTs, n=2705, RR intermediate or bad outcome 0.98 CI 0.86 to 1.11). Four studies found no effect for re-admission to Coronary Care Unit (4 RCTs, n=2644, RR 1.00 CI 0.77 to 1.30).Two other trials found intercessory prayer had no effect on re-hospitalisation (2 RCTs, n=1155, RR 0.93 CI 0.71 to 1.22).

Authors' conclusions
These findings are equivocal and, although some of the results of individual studies suggest a positive effect of intercessory prayer,the majority do not and the evidence does not support a recommendation either in favour or against the use of intercessory prayer. We are not convinced that further trials of this intervention should be undertaken and would prefer to see any resources available for such a trial used to investigate other questions in health care.

Plain language summary

Intecessory Prayer for the alleviation of ill health
Intercessory prayer is a very common intervention, used with the intention of alleviating illness and promoting good health. It is practised by many faiths and involves a person or group setting time aside to petition God (or a god) on behalf of another who is in some kind of need, often with the use of traditional devotional practices. Intercessory prayer is organised, regular, and committed. This review looks at the evidence from randomised controlled trials to assess the effects of intercessory prayer. We found 10 studies, in which more than 7000 participants were randomly allocated to either be prayed for, or not. Most of the studies show no significant differences in the health related outcomes of patients who were allocated to be prayed for and those who allocated to the other group.

Wednesday 15 July 2009

Fact Checking

Recently I drew your attention to an article in WIRED in August 2008 that declared the end of science as we know it HERE. It was clearly hubris and I have just found out that this was an understatement. See this interesting article from Peter Norvig who not only explains how he had been misquoted in the WIRED article, but also in passing pays homage to the legendary 'fact checking' of the New Yorker magazine.


Saturday 4 July 2009

R - the de facto Stats standard?

Here is an item on the R language in the The New York Times , highlighting the spread of R as the package of choice for academics and commercial users. And a related NYT blog item is here. One quote is interesting - "Intel Capital has placed the number of R users at 1 million".

Friday 3 July 2009

Data Mining

I have been reading up on using R for graphics and followed up on John Maindonald's book (HERE). He has some great resources on his website describing his view as a statistician on Data Mining (HERE) and I particularly liked this paper Data, science and new computing technology. From the
New Zealand Journal of Science 62 (2005): 126-128.