Category Archives: Science

Mapping Every Protein in the Human Body

Professor Neil Kelleher at Northwestern University gives a visionary talk about mapping an estimated 1 billion proteins in the human body. A lot of time in the media has been given to the sequencing of the human genome which has brought an astonishing rate of progress in medicine. This is not the final story though.

Genes are translated into proteins. If all of the genes in the human body are known then it should be possible to know all proteins translated from these genes. Knowing the protein correlate for each gene presents researchers with a target for the development of therapeutic agents.

The story is not yet finished. Proteins are further modified for instance by the addition of carbohydrates. The same gene may yield many versions of a final protein determined by the cellular environment in which the protein is created and these are referred to as proteoforms. Professor Kelleher’s vision is to characterise all of these protein variants and given the estimated number of proteoforms this seems a considerable challenge.

Professor Kelleher then takes us through some examples of how this could be useful in clinical diagnosis. Professor Kelleher is certainly visionary in his thinking. If his vision of a proteome is realised, the implications for medicine would be transformational.

History is replete with remarkable developments that have occurred only after a visionary reevaluation of an apparently unsolvable problem.

 

 

 

Perspective (Updated 31.8.13)

UniverseSciency* quote that didn’t fit into a single tweet so I thought it would find a home here.

Homo Sapiens are an extant genus of the tribe Hominini of the family Hominidae of the order Primates of the class Mammalia of the phylum Chordata of the kingdom Animalia living on and around a terrestrial planet orbiting a yellow dwarf star on the periphery of a barred spiral galaxy amongst an estimated 176 billion galaxies in the observable universe 13.798 billion years after the universe expanded from a point of singularity.

*sciency – from the Urban dictionary

Index: There are indices for the TAWOP site here and here Twitter: You can follow ‘The Amazing World of Psychiatry’ Twitter by clicking on this link. Podcast: You can listen to this post on Odiogo by clicking on this link (there may be a small delay between publishing of the blog article and the availability of the podcast). It is available for a limited period. TAWOP Channel: You can follow the TAWOP Channel on YouTube by clicking on this link. Responses: If you have any comments, you can leave them below or alternatively e-mail justinmarley17@yahoo.co.uk. Disclaimer: The comments made here represent the opinions of the author and do not represent the profession or any body/organisation. The comments made here are not meant as a source of medical advice and those seeking medical advice are advised to consult with their own doctor. The author is not responsible for the contents of any external sites that are linked to in this blog.

A Repository for Science Videos

OPEN SCIENCEVia ‘Free Technology for Teachers’ there is a repository of science videos established by the National Science Foundation. This is a curated collection which includes videos on designing molecules for the treatment of Alzheimer’s Disease through to the National Science Foundation and the Brain Initiative.

Index: There are indices for the TAWOP site here and here Twitter: You can follow ‘The Amazing World of Psychiatry’ Twitter by clicking on this link. Podcast: You can listen to this post on Odiogo by clicking on this link (there may be a small delay between publishing of the blog article and the availability of the podcast). It is available for a limited period. TAWOP Channel: You can follow the TAWOP Channel on YouTube by clicking on this link. Responses: If you have any comments, you can leave them below or alternatively e-mail justinmarley17@yahoo.co.uk. Disclaimer: The comments made here represent the opinions of the author and do not represent the profession or any body/organisation. The comments made here are not meant as a source of medical advice and those seeking medical advice are advised to consult with their own doctor. The author is not responsible for the contents of any external sites that are linked to in this blog.

A Talk About Releasing Your Inner Scientist

Nanoscientist Dr David Cramb gives an inspiring talk on how to release your inner scientist. He remarks on people’s innate curiosity, the relevance of curiosity for science and how this can be affected with time. Drawing a parallel with his efforts to learn and make music he suggests how those with an interest in science but who have become disconnected from it can reengage. Given the extensive applications of science, the video is relevant to a wide audience.

Index: There are indices for the TAWOP site here and here Twitter: You can follow ‘The Amazing World of Psychiatry’ Twitter by clicking on this link. Podcast: You can listen to this post on Odiogo by clicking on this link (there may be a small delay between publishing of the blog article and the availability of the podcast). It is available for a limited period. TAWOP Channel: You can follow the TAWOP Channel on YouTube by clicking on this link. Responses: If you have any comments, you can leave them below or alternatively e-mail justinmarley17@yahoo.co.uk. Disclaimer: The comments made here represent the opinions of the author and do not represent the profession or any body/organisation. The comments made here are not meant as a source of medical advice and those seeking medical advice are advised to consult with their own doctor. The author is not responsible for the contents of any external sites that are linked to in this blog.

An Example of Big Data Use in Medicine

IBM and the University of Los Angeles are working on using large datasets to improve the care of people with brain trauma. The brief video above gives an overview of this while this interview goes into more details about the structured and unstructured data that is being analysed so as to inform patient care.

Index: There are indices for the TAWOP site here and here Twitter: You can follow ‘The Amazing World of Psychiatry’ Twitter by clicking on this link. Podcast: You can listen to this post on Odiogo by clicking on this link (there may be a small delay between publishing of the blog article and the availability of the podcast). It is available for a limited period. TAWOP Channel: You can follow the TAWOP Channel on YouTube by clicking on this link. Responses: If you have any comments, you can leave them below or alternatively e-mail justinmarley17@yahoo.co.uk. Disclaimer: The comments made here represent the opinions of the author and do not represent the profession or any body/organisation. The comments made here are not meant as a source of medical advice and those seeking medical advice are advised to consult with their own doctor. The author is not responsible for the contents of any external sites that are linked to in this blog.

Cameron Neylon on Open Science

Scientist Cameron Neylon is an advocate for open science and in this video (from the Open Repositories 2012 conference) he talks about many important aspects of open science. Neylon gives examples of scientific communities that have transformed research methodologies through online networks and accelerated analysis of data in the process. He also looks at the issue of increasing the impact of open science through open science networks. There is a question and answer session at the end.

Index: There are indices for the TAWOP site here and here Twitter: You can follow ‘The Amazing World of Psychiatry’ Twitter by clicking on this link. Podcast: You can listen to this post on Odiogo by clicking on this link (there may be a small delay between publishing of the blog article and the availability of the podcast). It is available for a limited period. TAWOP Channel: You can follow the TAWOP Channel on YouTube by clicking on this link. Responses: If you have any comments, you can leave them below or alternatively e-mail justinmarley17@yahoo.co.uk. Disclaimer: The comments made here represent the opinions of the author and do not represent the profession or any body/organisation. The comments made here are not meant as a source of medical advice and those seeking medical advice are advised to consult with their own doctor. The author is not responsible for the contents of any external sites that are linked to in this blog.

Doing Science Using Open Data – Part 6: Modelling Populations

In this 6th part of the series on using open data for science I’ve take a slight diversion to look at populations and the issue of sampling. This was prompted by a look at the UK mid-2011 Census data shown in the graph below.

Figure 1: Summation of male and female figures for each age from mid-2011 Census. Red bars represent the age group 45-65 and the blue bars represent the age group 16-44

What were going to do is look at the UK population and build a mathematical population and build a model for the populations we’ve looked at in the previous posts. Just to recap, when we compared two populations there are a number of statistical methods for doing this which are dependent on the characteristics of the population. For a normally distribution population we can define this population by the mean and standard deviation. As discussed in previous posts the populations in this post from the census study in mid 2011 which are not normally distributed. In the first segment aged 16-44 there is a somewhat homogenous group?? whilst in the group 45-65 there is a right skewed distribution that is the numbers for each year get progressively smaller.

In the third part in this series I included some of the data from the mid-2011 Census which I will reproduce here to support the subsequent discussion. Summing the male and female figures we get the following results for ages 16 through to 44

680,979
706,234
711,491
741,667
765,895
757,901
757,295
771,297
756,449
768,415
774,921
759,889
768,860
770,810
778,986
782,510
751,251
700,825
690,775
702,024
716,419
729,013
761,347
794,300
820,805
800,550
821,037
819,650
832,297

For ages 45-65 we get the following results

832,727
838,064
831,041
813,798
797,077
770,066
739,859
723,861
708,371
682,824
659,795
637,073
641,145
634,399
618,132
623,508
638,118
655,668
694,644
754,834
583,734

The total estimated population in England and Wales in Mid-2011 for the age group 16-44 is

21993892

and for the age group 45-65 is

15711035

So if we move firstly to the population aged 45-65. This population has a value that begins with 832,727 people aged 45 and decreases to 583,734 at age 65 . First recall that the x-axis represents age and the y-axis is the number of people in each age group. The population can be approximately described by a line of decreasing slope.  Now if we’re going to model this we’re going to need to understand what the relationship is between x and y. Quite obviously as x increases y decreases and the relationship is described by y = -x. Looking at the graph above this doesn’t seem intuitive. None of the y values are negative. However if the graph began at (0,0) then it would become negative as x increased. The reason that this doesn’t happen in the above graph is that the line y = -x is translated in a positive direction along the y-axis. So in other words (I will take out the negative sign at this stage as it will be dealt with by the coefficient a)

y =  x + c

In addition to this, rather than a straight line with a unit gradient (i.e for every unit increase along the x-axis there is a unit increase along the y-axis) the line has a gradient which we have yet to determine. For the sake of convenience I will refer to this as

y =  a x + c

There is a simple introduction to lines and slopes below.

Our job now is to find out what those two variables a and c are. This is going to be an approximation. Turning first to people aged 45

y =  a x + c

832,727 =  44 a + c

and for the age 65

583,734 =  65 a + c

We have two equations that we have to solve and two sets of values to do this. Since

832727 = 44 a + c

44 a = 832727 – c

a = (832727-c)/44

Now from the original equations we know that

583,734 = 65 a + c

and therefore substituting

a = (832,727-c)/44

we get

583734 = 65/44 (832727-c) + c

Multiplying out we get

583734 =  (1 – 1.477)c + 1230164.89

– 646430.88636 = -0.477c

c = 1354426.6

Substituting back into the original equation

583,734 = 65 a + 1354426.6

Rearranging we get

(583,734 – 1354426.6)/65 = a

a = -11856.81

Substituting the values for a and c into the original equations above, the reader will be see that these values solve the equations. The numbers have been rounded up. Indeed rounding to the nearest number we arrive at the following equation

y = -11857 x + 1354427

This equation approximately describes the UK mid-2011 Census data for the age group 45-65 where y is the total population for each age and x is the age in years within the given range.

Appendix

Doing Science Using Open Data – Part 1

Doing Science Using Open Data – Part 2

Doing Science Using Open Data – Part 3

Doing Science Using Open Data – Part 4

Doing Science Using Open Data – Part 5

Index: There are indices for the TAWOP site here and here Twitter: You can follow ‘The Amazing World of Psychiatry’ Twitter by clicking on this link. Podcast: You can listen to this post on Odiogo by clicking on this link (there may be a small delay between publishing of the blog article and the availability of the podcast). It is available for a limited period. TAWOP Channel: You can follow the TAWOP Channel on YouTube by clicking on this link. Responses: If you have any comments, you can leave them below or alternatively e-mail justinmarley17@yahoo.co.uk. Disclaimer: The comments made here represent the opinions of the author and do not represent the profession or any body/organisation. The comments made here are not meant as a source of medical advice and those seeking medical advice are advised to consult with their own doctor. The author is not responsible for the contents of any external sites that are linked to in this blog.