This document discusses issues with reproducibility in scientific research. It provides examples of studies that could not be reproduced, including a case where only 6 out of 53 landmark cancer studies could be validated. It advocates for more transparency through open data, open access, and open source policies to improve reproducibility and rebuild trust in science. Open and reproducible research practices like open notebook science are presented as ways to achieve faster, more reliable science.
12. Eight committees investigated the allegations and
published reports, finding no evidence of fraud or scientific
misconduct.
However, the reports* called on the scientists to avoid any
such allegations in the future by taking steps to regain
public confidence in their work, for example by opening up
access to their supporting data, processing methods and
software, and by promptly honouring freedom of
information requests.
* Archana Venkatraman, "Data Without the Doubts". Information World Review
13. Andrew Wakefield’s study,
linked the measles, mumps
and rubella vaccine to autism.
Vaccination rates in the
developed world plummeted
after the study’s publication
and a heated anti-vaccination
movement persists today.
17. Science has lost its way, at a big cost to humanity
Researchers are rewarded for splashy findings, not for double-checking
accuracy. So many scientists looking for cures to diseases have been
building on ideas that aren't even true.
A few years ago, scientists at the Thousand Oaks biotech
firm Amgen set out to double-check the results of 53 landmark papers in
their fields of cancer research and blood biology.
The idea was to make sure that research on which Amgen was spending
millions of development dollars still held up. They figured that a few of
the studies would fail the test — that the original results couldn't be
reproduced because the findings were especially novel or described
fresh therapeutic approaches.
But what they found was startling: Of the 53 landmark papers, only six
could be proved valid.
http://www.latimes.com/business/la-fi-hiltzik-20131027,0,1228881.column#axzz2ix1w9zGf
18.
19.
20. A special challenge for science writers covering research
today arises from science’s growing credibility problem. It
stems from the cumulative effect of errors and exaggerations
that has fueled a recent rise in retractions, misconduct, and
fraud among peer-reviewed researchers.
For reporters covering major scientific developments – from
the search for alien life and genomics, to particle physics,
climate change and cancer — it can be difficult to distinguish
error from fraud, sloppiness from deception, eagerness from
greed or, increasingly, scientific conviction from partisan
passion. Findings in fields from climate change to vaccines
can also be deceptively cherry-picked in service of a political
cause.
57. Collection: Open Data
source data points curated values source year data type
Bell 2483 1631 1995 donated-CC0
Bergstrom 277 277 2003 open
MDPI-Karthikeyan 4450 4084 2005 open
Hughes 287 262 2008 open
Oxford-MSDS 3217 1481 2010 open
Drugbank 875 875 2011 open
Griffiths 3757 278 2011 donated-CC0
Alfa Aesar 12986 8739 2011 donated-CC0
PHYSPROP 11645 9694 2011 donated-CC0
ONS 471 471 2012 open
27792 curated measurements
for 19515 compounds
58. Curation is…
…lots of hard, tedious work
(Jean-Claude Bradley and Antony Williams)
Antony Williams – RSC ChemSpider
61. PHYSPROP Errors: Structure displayed is for the neutral
compound dopamine but the associated CAS Number and
chemical name in the file are for the hydrobromide salt.
62. unit errors: Kelvin/Celsius, Fahrenheit/Celsius
bad SMILES (non-rendering, hypervalency)
salts associated with SMILES for free base
using boiling point for melting point
69. Straight chain carboxylic acids from 1 to 10 carbons
Straight chain alcohols from 1 to 10 carbons
Comparison of model with
double+ validated measurements
70. Cyclic primary amines from 3 to 6 carbons
cyclobutylamine flagged for measurement
only single source available
76. Can the solvents used to recrystallize compounds in
organic teaching labs be improved?
Trans-dibenzalacetone
Aldol condensation between two molecules of
benzaldehyde and one molecule of acetone
[Matthew McBride: Undergraduate Research Assistant - Drexel]
77. First recrystallized in ethyl acetate in 1906: Straus
and Ecker, Ber. 39, 2988 (1906)
Recrystallized in ethyl acetate in Organic Syntheses
80. How does it work?
1. Look up the solvent boiling point
2. Look up the room temperature solubility or predict it via measured or
predicted Abraham descriptors
3. Look up the solute melting point or predict it via a model
4. Use the melting point and the solubility at room temperature to predict
the solubility at boiling
5. Calculate the predicted recrystallization yield
81. Lists solvents and their predicted recrystallization yield.
Prediction is generated by the temperature dependent
solubility curves.
82. ethyl acetate (predicted yield of 72%) vs ethanol
(predicted yield of 93%)
ethyl acetate
ethanol
0.09M
1.1M
0.62M
2.06M
84. Derivatives of dibenzalacetone may be synthesized
by altering the aldehyde used
From a library of derivatives, the following
compound was the top hit for the docking site of
Taxol
Uses phenanthrene-9-carboxaldehyde
85. Perform a Reaxys search to determine availability
of synthesis procedures
No results
[Matthew McBride: Undergraduate Research Assistant - Drexel]
86. Used methanol and benzene
Melting Point: 264-265°C
(http://usefulchem.wikispaces.com/EXP286)
[Matthew McBride: Undergraduate Research Assistant - Drexel]
88. Acknowledgements
Jean-Claude Bradley (Drexel)
Cameron Neylon (Advocacy Director at PLOS)
Antony Williams (RSC ChemSpider)
Drexel research assistants: Evan Curtin and Matthew
McBride
ORU research assistants: David Bulger, Daryl Charron,
Lizzie Clark, Lacey Condron, Samantha Gaines, Alejandro
Hernandez, Maria Hernandez, Jesse Patsolic, and
Matthew Wilson
Editor's Notes
http://usefulchem.wikispaces.com/D-EXP022
From a library of derivatives, it was the hop hit for the docking site of taxol