ChEBI compounds can be found below.

Structure	ChEBI ID	Chemical Formula	Name
	CHEBI:219639	C21H27F3O2	6,6,9-Trimethyl-3-(5,5,5-trifluoro-pentyl)-6a,7,10,10a-tetrahydro-6H-benzo[c]chromen-1-ol (5′-F3-delta8-THC)
	CHEBI:219603	C21H29FO2	3-(5-Fluoro-pentyl)-6,6,9-trimethyl-6a,7,10,10a-tetrahydro-6H-benzo[c]chromen-1-ol (5′-F-delta8-THC)
	CHEBI:164237	C21H30O2	6,6,9-Trimethyl-3-pentyl-6a,7,8,10a-tetrahydro-6H-benzo[c]chromen-1-ol (delta9-THC)
	CHEBI:566631	C37H54O4	alpha-Cadinyl delta9-Tetrahydrocannabinolate
	CHEBI:566632	C37H54O4	gama-Eudesmyl delta9-Tetrahydrocannabinolate
	CHEBI:566609	C32H46O4	alpha-Terpenyl delta9-Tetrahydrocannabinolate
	CHEBI:566610	C32H46O4	beta-Fenchyl delta9-Tetrahydrocannabinolate
	CHEBI:566618	C32H46O4	alpha-Fenchyl delta9-Tetrahydrocannabinolate
	CHEBI:566619	C32H46O4	epi-Bornyl delta9-Tetrahydrocannabinolate
	CHEBI:566620	C32H46O4	Bornyl delta9-Tetrahydrocannabinolate
	CHEBI:566630	C32H46O4	4-Terpenyl delta9-Tetrahydrocannabinolate
	CHEBI:566636		delta9-tetrahydrocannabinolic acid A

Several of these compounds have been tested in various brain regions against the two known canabinoid receptors and from the Ki database we find that there is more data for CB1 (345), than the CB2 (173). Results are also organized by species and brain region with rat (296 results) and human (192) tested most frequently, followed by mouse (18), zebra finch (8) and newt (5) data.

 

Pathways

Wiki pathways, a collaborative platform from UCSF, lists the following pathways for CNR1 and CNR2:

Pathway Name

• GPCRs, Class A Rhodopsin-like (11)
• Small Ligand GPCRs (11)
• GPCRs, Other (3)

Gene Symbol

• CNR2 (7)
• CNR1 (6)

Organism

• Mus musculus (5)
• Pan troglodytes (5)
• Rattus norvegicus (5)
• Homo sapiens (4)
• Bos taurus (2)
• Danio rerio (2)
• Gallus gallus (2)

 

MultiMedia Information

Scientists studying endo- and exo-cannabinoids have written hundreds of blogs. Most of these focus on cannabis risks or the treatment of various disorders. A quick survey of these blogs indicates that there are links to Fragile X syndrome, multiple sclerosis, depression and decreases in intelligence on standardized tests. In addition, many scientists study the risk of motor vehicle accidents and possible interactions of mothers’ canabinoid exposure and the proclivity of the offspring toward opiates, but surprisingly some have also reported a Marijuana-Borne Salmonella Outbreak and poisoning of workers from herbicides used to kill the plants.

A few video talks and interviews with leading researchers are also available (see several examples below).

_____________________________________________________________________________

NIHVideo		Molecular Dissection of Cannabis Sensitivity in the Developing Brain		Tibor Harkany, PhD, Department of Medical Biochemistry and Biophysics, Karolinska Institute
NIHVideo		New Developments in Cannabinoid Research: The Path from Plant to Modern Prescription Medicine		Guy, Geoffrey W. National Institutes of Health (U.S.)
The Guardian: Science Videos		Cannabis ‘more harmful to under-18s than adults’ – video
NIHVideo		Brain Stress Systems and Addiction		Koob, George F. National Institutes of Health (U.S.)

 

Funding Sources

Not surprisingly, NIDA funds most research on cannabis, but a few current grants are also given by NIMH, Alcohol, and NINDS. The breakdown of the number of recent grants by institute follows: national institute on drug abuse (375), national institute of mental health (26), national institute on alcohol abuse and (26), national institute on aging (11),  and many others.

From older grants (Research Crossroads dataset covering both federal and foundation grants) we find that many institutes and foundation have given out grants related to the cannabinoids, including:

• National Institute on Drug Abuse(NIDA) (2937)
• National Center for Research Resources(NCRR) (152)
• National Institute of Neurological Disorders and Stroke(NINDS) (90)
• National Institute on Alcohol Abuse and Alcoholism(NIAAA) (64)
• National Institute of Mental Health(NIMH) (57)
• National Institute of General Medical Sciences(NIGMS) (52)
• National Cancer Institute(NCI) (33)
• National Eye Institute(NEI) (33)
• National Institute of Allergy and Infectious Diseases Extramural Activities(NIAID) (15)
• National Institute of Child Health & Human Development(NICHD) (15)
• Medical Research Council (UK) (12)
• National Heart, Lung, and Blood Institute(NHLBI) (12)
• CORDIS (11)
• National Institute of Environmental Health Sciences(NIEHS) (9)
• National Center for Complementary and Alternative Medicine(NCCAM) (7)
• National Institute of Diabetes and Digestive and Kidney Diseases (7)
• National Institute on Aging(NIA) (7)
• Fogarty International Center(FIC) (5)

Our search also reveals that even private funders like the American Diabetes Association also gave out a grant focusing on the therapeutic effects of endogenous cannabinoids in diabetic retinopathy.

 

Diseases and Clinical Studies

There are few diseases directly associated with Marijuana, however Pubmed health mentions four, including:

Marijuana intoxication

Aspergillosis, which is an infection or allergic response due to the Aspergillus fungus. Aspergillosis is caused by a fungus (Aspergillus), which is commonly found growing on dead leaves, stored grain, compost piles, or in other decaying vegetation. It can also be found on marijuana leaves. Although most people are often exposed to aspergillus, infections caused by the fungus rarely occur in people who have a normal immune system. The rare infections caused by aspergillus include pneumonia and fungus ball (aspergilloma).

Lung cancer – non-small cell, which mentions that “research shows that smoking marijuana may help cancer cells grow, but there is no direct link between the drug and developing lung cancer.”

Paraquat poisoning, which describes paraquat (dipyridylium) as a highly toxic weed killer once promoted by the United States for use in Mexico to destroy marijuana plants. Research found that this herbicide was dangerous to workers who applied it to the plants. This article discusses the health problems that can occur from swallowing or breathing in Paraquat.

NIF searches across two sources of clinical data, and the US based ClinicalTrials.gov contains information about 294 clinical trials, but the European based EU Clinical Trials Register finds only 27 additional trials.  Below you can find the main conditions, interventions and sponsors for the clinical trials, with numbers indicating the number of clinical trial results.

Conditions

• Marijuana Dependence (15)
• Marijuana Abuse (13)
• Multiple Sclerosis (11)
• Cannabis Dependence (10)
• Healthy (8)
• Marijuana Smoking (6)
• Pain (5)
• Schizophrenia (4)
• Schizophrenia;Schizoaffective Disorder (4)
• Substance-Related Disorders

Intervention

• Behavioral: Behavior Therapy (6)
• Drug: Dronabinol (6)
• Drug: Cannabis (4)
• Drug;Drug: Sativex®;Placebo (4)
• Drug: GW-1000-02 (3)
• Drug: Nabilone (3)
• Drug: Smoked Cannabis (3)
• Drug;Drug: GW-1000-02;Placebo (3)

Sponsored By

• National Institute on Drug Abuse (NIDA); NIH (23)
• GW Pharmaceuticals Ltd.; Industry (15)
• New York State Psychiatric Institute;National Institute on Drug Abuse (NIDA); Other;NIH (9)
• Center for Medicinal Cannabis Research; Other (7)
• National Institute of Mental Health (NIMH); NIH (6)
• Yale University; Other (6)

 

Inference Data

The Clinical Toxogenomics Database (CTD) includes data about genes, pathways and diseases that have been found to be statistically associated with cannabinoids. The data are not from direct assertions, so they should be taken with a certain degree of skepticism. However, possibly interesting interactions with the following genes, diseases and pathways have been asserted.

Microarray and Gene Expression Data

The Gene Expression Omnibus (GEO) contains data from 5 studies having to do with cannabinoids.

One of those studies was analyzed in significant detail by Gemma, which tells us that the study which specifically targeted an animal model for cutaneous contact hypersensitivity, showed that mice lacking both known cannabinoid receptors display exacerbated allergic inflammation. The study looked at CNR knockout mice and the main experimental factors were dinitrofluorobenzene vs. Control_group, and the Cnr1-/-/Cnr2-/- vs. C57BL/6J (knockout vs control).

The drug related gene database, reports on several studies including a heroin withdrawl / cannabidol withdrawl interaction study showing some interactions in the caudoputamen. The brain regions, experimental conditions and organisms most commonly studied are listed below:

Brain Region

• Anterior prefrontal cortex (556)
• Dorsolateral caudoputamen (8)
• Medial caudoputamen (8)
• Mid-lateral caudoputamen (8)
• CA1 stratum lacunosum moleculare (5)
• CA1 stratum oriens (5)
• CA1 stratum radiatum (5)
• CA3 stratum lucidum (5)
• CA3 stratum oriens (5)
• CA3 stratum radiatum (5)

Exp vs Control

• Cocaine + THC + PCP vs. Control (139)
• Cocaine vs. Control (139)
• PCP vs. Control (139)
• THC vs. Control (139)
• Delta9 THC vs. 1:1:18 solution of ethanol, emulphor, and saline (17)
• Alpha7 nicotinic acetylcholine + cannabinoid receptor 1 vs. Alpha7 nicotinic acetylcholine (9)

Organism

• Human: , 13-64 years Adolescent – Adult human (556)
• Sprague Dawley Rat: Male, Adult 200-250 g (43)
• Long Evans rat Rat: Male, 230-250 g at the beginning of the experiment (30)
• Mouse: , (17)
• Sprague Dawley Rat: Male, Adult rat 380-410 g (2)

Protocol Type

• dna microarray (558)
• immunohistochemistry (47)
• in situ hybridization / immunohistochemistry (18)
• in situ hybridization / double in situ hybridization (16)
• in situ hybridization /double in situ hybridization (9)

In mice, the brain structures that express cnr1 and cnr2, based on data from the mouse genome informatics database, the alen brain atlas and gensat are:

• hypothalamus (10)
• olfactory bulb (10)
• thalamus (10)
• cerebellum (9)
• cerebral cortex (9)
• midbrain (9)
• pons (8)
• amygdala (7)
• hippocampus (7)
• pallidum (7)
• hippocampal formation (6)

• lateral septal complex (6)
• anterior olfactory nucleus (5)
• basal ganglia (5)
• corpus striatum (5)
• diencephalon (5)
• entorhinal cortex (5)
• globus pallidus (5)
• hindbrain (5)
• inferior colliculus (5)

Most common assays are:

• rt-pcr (976)
• bac-cre recombinase driver (38)
• rna in situ hybridization (34)
• rna in situ (26)

The age of the organism:

• postnatal week 6-8 (732)
• postnatal (244)
• adult (53)
• embryonic day 14.5 (26)
• p7 (19)

Brain Volume and Brain Activation Foci Data

Based on a publication in 2010, the cerebellar volume of marijuana abusers of 18 years of age appears to be significantly smaller than the norm. The norm is established by looking at the volumes reported from many publications.

The brain activation foci from SumsDB involved in marijuana use or abuse are shown as gray dots on the brain below. Each gray dot represents a coordinate from a study cataloged by SumsDB that involves cannabis. These have been pulled from the WebCaret software, from the laboratory of David VanEssen, and are accessible by clicking the “View on Brain” button within the SumsDB data result. Below, we are showing several views of the same result set, because not all points are visible from any one view of the brain, suggesting that there is no unified brain region involved cannabis abuse rather many regions are involved.

Medial View

Posterior View

Imaging Data

The Cell Image Library has several data sets from Margaret I. Davis, mainly of interneurons expressing EGFP from the 5HT3 receptor promoter (Tg(Htr3a-EGFP)DH30Gsat, www.gensat.org) colabelled for the CB1 cannabinoid receptor.

The image below is from the pyramidal cell layer in hippocampal CA1.

The figures show the distribution of interneurons expressing EGFP from the 5HT3 receptor promoter (Tg(Htr3a-EGFP)DH30Gsat, www.gensat.org) in the dorsal hippocampus colabelled for the CB1 cannabinoid receptor (red) and counterstained with DAPI (blue) to show the cell layers. In this experiment EGFP expression was amplified with chicken anti-GFP (Abcam, 1:2000); cell bodies and fibers are present throughout all layers of the hippocampus but enriched in the hilus and stratum lacunosum moleculare (see associated images). CB1 immunoreactivity (L15 rabbit polyclonal 1:200, K. Mackie) is prominent in the terminals of basket cells synapsing in the pyramidal cell layer. CB1 is also enriched in axons with distinct intensities in the inner and outer molecular layer of the dentate gyrus. CB immunoreactivity is also present in the stratum radiatum and stratum lacunosum moleculare.

The data above can be complemented by 168 images gathered by Gensat from this mouse, generated by that project.

Resources

Animals, antibodies, databases as well as a game useful for teaching undergraduates are available from various sources.

The mouse line generated by Gensat (images above) is now available from the MMRRC resource, where two founder lines of knock out mice are available. The International Mouse Resource Center (IMSR) lists several other mice that may be available to the research community.

The Antibody Registry, our in house antibody aggregator, which aims to serve the scientific community by providing a set of unique identifiers for commercial and non-commercial antibody reagents, lists 242 antibody reagent offerings related to cannabinoids from over 10 vendors.

The NIF registry does not encode many resources that are specifically devoted to cannabinoids, but does note that several resources mention cannabis in their description including:
University of California at San Diego, Center for Medicinal Cannabis Research Resource Type: institutional portal
The Center for Medicinal Cannabis Research (CMCR) will conduct high quality scientific studies intended to ascertain the general medical safety and efficacy of cannabis products and examine alternative forms of cannabis administration. The Center will be seen as a … See full record: nif-0000-10503

This is a question asked by Alan Alda, a tireless advocate for clear communication of science to the public. He has been the host of the PBS series “Scientific American Frontiers” for many years and has worked since 2005 on a novel and amazing idea: scientists should drop the jargon and actually try to communicate clearly to the public.

Apparently if you drop the big words that are relatively inscrutable, most medical procedures begin to sound a little more comprehensible. Alan used the example of the end-to-end anastomosis, an inscrutable surgery that he performed on M.A.S.H. often, but when a doctor had to perform this same surgery on him, it was explained a little more clearly, in that a part of the colon that had gone bad needed to be removed and the healthy ends needed to be re-attached.

This does not take a genius to understand, but the terminology in medicine and science in general can be so full of jargon that scientists in adjacent fields have trouble. In fact, here is a sentence that I wrote, but would be hard pressed to ask anyone outside of a small field of neuroscientists to interpret correctly “In CNQX, ACPD only decreased EPSPs, but APV or bicuculline did not change the effect of ACPD.” This was not meant for a general audience, but I can see that we must do better in explaining our findings to each other, if not the general public. Why have we built a system that has become so difficult to understand?

If we think that this system is not a good system, like Alan Alda suggests, what can be done to change this?

Alan, for one is not sitting around asking questions, this year at Stony Brook University he will be starting a new chapter in his illustrious career as an academic. In 2009, he launched the “Alan Alda Center for Communicating Science” and has been touring universities, teaching workshops and campaigning since. This is a great effort and I for one, wish him the best of luck and hope that more scientists can think and talk clearly about science.

For more, see:

http://www.centerforcommunicatingscience.org/alan-alda/

by Maryann E Martone

I was speaking with a colleague recently who, like many of us, had experienced the frustration of trying to support his on-line resources.  He has assembled a comprehensive on-line resource, it is used by the community and was used by others to publish their studies.  It is not Genbank or EBI;  it is one of the thousands of on-line databases created by individuals or small groups that the Neuroscience Information Framework and others have catalogued.  My colleague has spent years on this resource, pored over hundreds of references and entered close to a million statements in the database.  By many means, it is a successful resource.  But in the grant review, he was criticized for not having enough publications.  I experienced the same thing in a failed grant for the resource that I had created, the Cell Centered Database.  In fairness, that was not the most damning criticism, but it just seemed so very misplaced. I had succeeded in standing up and populating a resource, well before there was any thought of actually sharing data.  People used the database and published papers on it, but apparently I should have been spending more time writing about it and less time working on it.

The problems of creating and maintaining these types of resources are well known and were discussed at Beyond the PDF2:  to be funded, you have to be innovative.  But you don’t have to be innovative to be useful.  To quote or paraphrase Carole Goble at the recent conference,  “Merely being useful is not enough.”

But presumably there is a threshold of perceived value where “merely being useful” is enough.  I am thinking of the Protein Databank or Pub Med.  These resources are well funded and also well used but hardly innovative.  I am guessing that many of the resources like my colleague and I created were started with the hope that they would be as well supported and integral to people’s work as the PDB or Pub Med.  But the truth is, they are not in the same class.  But they are still valuable and represent works of scholarship.  We are now allowed to list them on our biosketch for NSF.  So my question to you is:  how do we evaluate these thousands of smaller databases?

Ironically, our peers have no trouble evaluating an article about our databases, but they have much more trouble evaluating the resource itself.  How does one weigh 30,000 curated statements against 1 article?  What level of page views, visits, downloads and citations make a database worthwhile?  If my colleague had published 10 papers, the reviewers wouldn’t have likely checked how often they were cited, particularly if they were recent.  What is the equivalent of a citation classic for databases?  If you don’t have the budget of NCBI, then what level of service can you reasonably expect from these databases?  I thought that the gold standard was a published study that utilized your database to do something else, by a group unconnected to you.  Grant reviewers found that unconvincing.  Perhaps I didn’t have enough? But how many of these do you need, relative to the size of your community,  and on what time frame should you expect them to appear?  Sometimes studies take years to publish.  Do they need to be from the community that you thought you were targeting (and whose institute may have funded your resource) or does evidence from other communities count?

So perhaps if we want to accept databases and other artefacts in lieu of the article, we should help define a reasonable set of criteria by which they can be evaluated.  Anyone care to help here?

A number of groups, from libraries and universities and academic projects are striving to implement flexible data management systems in order to harness the latest and greatest in semantic web technologies striving to integrate and facilitate breakthrough interdisciplinary analysis.

It is known that every lab, every individual research group (regardless of the discipline) has developed internal data management systems that “work” (i.e. literature & data collection > excel > stats > graphing > word processer) but what has your lab found useful and what are your biggest frustrations?

Please feel free to comment below, or join the discussion on ResearchGate.

…Well now you can.

Two Planning Meetings: Public Access to Federally-Supported Research and Development Data andPublications

National Academy of Sciences
Meetings are free and open to the public, but registration is required

Public Comment Meeting: PUBLICATIONS

14 May 2013, 9 a.m. – 5 p.m.
15 May 2013, 9 a.m. – 12 p.m.
National Academy of Science
Auditorium
2100 Constitution Avenue
Washington DC 20418
Register Here

On 22 February 2013, the Office of Science and Technology Policy (OSTP) issued a memorandum to the heads of executive departments and agencies, directing them to “develop a plan to support increased public access to the results of research funded by the Federal Government.”

As part of this planning process, a group of cooperating federal agencies has requested that the National Research Council (NRC) Division on Behavioral and Social Sciences and Education (DBASSE) organize this meeting to draw in representatives of all stakeholder groups and interested parties.  The purpose of the meeting is to allow those who wish to do so an opportunity to provide input into the development of acceptable models of public access to the outputs of federally supported research and development.

The National Academy of Science, in keeping with its 150-year tradition of service to the nation, will provide an unbiased forum in which all views may be heard.  Time constraints may require that selection be made among the many who will apply to speak; every effort will be made to assure that those who are selected are representative of all viewpoints.  In addition, all written statements that are submitted through this registration site will be passed on to the sponsors (no other written materials will be accepted).

The meeting will be webcast, which means that the proceedings can be followed by stakeholders around the world, and, after the meeting is over, the video will be posted for easy access and convenience.

Questions about the meeting should be directed to: PublicAccess-Publications@nas.edu.

Public Comment Meeting: DATA

16 May 2013, 9 a.m. – 5 p.m.
17 May 2013, 9 a.m. – 12 p.m.
National Academy of Science
Auditorium
2100 Constitution Avenue
Washington DC 20418
Register Here

On 22 February 2013, the Office of Science and Technology Policy (OSTP) issued a memorandum to the heads of executive departments and agencies, directing them to “develop a plan to support increased public access to the results of research funded by the Federal Government.”

As part of this planning process, a group of cooperating federal agencies has requested that the National Research Council (NRC) Division on Behavioral and Social Sciences and Education (DBASSE) organize this meeting to draw in representatives of all stakeholder groups and interested parties.  The purpose of the meeting is to allow those who wish to do so an opportunity to provide input into the development of acceptable models of public access to the outputs of federally supported research and development.

The National Academy of Science, in keeping with its 150-year tradition of service to the nation, will provide an unbiased forum in which all views may be heard.  Time constraints may require that selection be made among the many who will apply to speak; every effort will be made to assure that those who are selected are representative of all viewpoints.  In addition, all written statements that are submitted through this registration site will be passed on to the sponsors (no other written materials will be accepted).

The meeting will be webcast, which means that the proceedings can be followed by stakeholders around the world, and, after the meeting is over, the video will be posted for easy access and convenience.

Questions about the meeting should be directed to: PublicAccess-Data@nas.edu.

This is a fun article about the injection of human stem cells into early mouse pups.

The stem cells injected formed astrocytes that were more human like than mouse like and the outcome? Smarter mice. This brings up a slew of questions, the ethics of what is it to be a mouse, how human is a critter before it is considered a human, but also interestingly, does the neuron or the glial cell really determine how smart we are?

I can almost hear Glenn Hatton, smiling from the great beyond and still telling me “its all about the glia”.

Dear electrophysiologists,

If you could spare about 5 minutes of your time, the INCF electrophysiology task force is attempting to survey the landscape of definitions of the action potential. The main interest here is to determine how working physiologists view it, is it an event, property of the membrane or a process?

The following link will take you to a google-survey, click here or follow this link:

https://docs.google.com/forms/d/1RjFbxxQ1APZ-wZ3qRudgLMF7B6x6C0E5QhATqd4JYxQ/viewform?sid=afb1a6cad01cf6e&token=3MImFj0BAAA.ISZ-71P88ISEhUfd4WLe_Q.mHMDtq5u5_29UwuZ1EYquw

The results will be stored on a google spreadsheet and the answers will be used to design a relevant knowledge model to describe electrophysiology data with the Experimental Neurophysiology Ontology (ENO).

Thank you in advance for any help you can provide.

By Anita Bandrowski

This is not a blog post that I ever imagined writing.

Likely many of you have heard that there has been a tragedy in that on January 11, 2013 a very talented young computer programmer and activist, Aaron Swartz, took his own life in New York city. The young man, was one of the bright starts of the computer generation, added significantly to Reddit and the RSS specification among other work (started contributing at age 14!).

His later life, by this I mean his early 20′s, was spent in fighting the closed world of science. He was the founder of Demand Progress, an online activist group that was able to mobilize enough like minded thinkers and used this influence to black out wikipedia and google (partially) culminating in the defeat of the SOPA/PIPA bills last year.

He was very opposed to the current system for publishing science, in fact he broke the law in protest. He did not intend to make money from his criminal activities, but he certainly broke the law. He did not hurt anyone, his crime consisted of putting a laptop into a small closet in the MIT library and downloading millions of articles from the JSTOR archive. He believed, as many including the former head of the National Institutes of Health do, that information, especially information generated as a result of billions of dollars of tax-payer money should not be the exclusive right of a corporation. He believed that scientific knowledge was the legacy of human endeavor and as such it should be open to all humans. In this, he was not alone, but he was braver or at least more industrious than most. He infringed the copyright agreement of a group of for profit cooperations and told people about it.

For this crime, he was being sued in criminal court and was facing 35 years in prison as well as a million dollar fine.

He took his own life and the case was dropped by the prosecution.

Is this what it takes to reform a broken system of scientific publishing?

In my opinion, he is a martyr for a cause, I just never imagined that reforming scientific publishing practices would require a martyr. In the many thousands of years that scholars thought interesting things and put them on paper for others to read, there have been many cases where some brave soul had to protect that knowledge. Perhaps, Aaron is a modern Hypatia?

Regardless of his place in history, his life and death should give us pause on what the President termed a “national day of service.” For my part, I think that I will add my currently unrepresented publications to the National Library of Medicine’s PubMed Central and consider publishing in only the open access subset of PMC from now on. It is certainly not a big gesture, but possibly no less relevant than expressing outrage at the prosecutors of Aaron’s case.

by Maryann Martone

A recent post at the London School of Economics Social Science Impact blog on “Finding the time to blog” reminded me that I wanted to write a blog about why I started to blog. The use of social media and its proper place in academic communications is being discussed in many circles. Over at FORCE11, we aggregate quite a few blog feeds like the one from LSE where these issues are thoroughly covered. I wanted, however, to share a personal perspective. Like many scientists, I suspect, I was at first reluctant to blog. I did write a few posts for the NIF blog when we started it up, but then stopped because “It takes too much time”. Each blog took me several weeks before I was happy with it and, as is well advertised, blogs don’t count towards academic promotion, etc. So if I was going to spend that amount of time, I might as well spend it towards something that does count: writing papers, giving talks, training, teaching, networking and, oh, doing research. Besides, who would want to hear what I had to say?

Well, the astute reader might have noted that many of our rewarded activities involve someone (funders, conference organizers, students) actually paying to hear what we have to say. And, the astute reader might also note that a blog is a much more effective communication vehicle than most of these for accomplishing these tasks. I started to blog for real when I realized that a blog is my communication with the world. A lot of money has been invested in me as a vehicle for knowledge acquisition and integration. The more I share that with the world, the better I do my job. A blog is not a learned treatise which needs to carefully consider all angles, acknowledge all references in a specified format and go through rounds and rounds of editing to craft the language so as to offend nobody with unsupported statements. A blog is a written yet highly interactive version of the type of conversation I engage in every day with students, colleagues, audiences. It is my thoughts on a topic, developed over a lifetime of active inquiry, open to correction and discussion. You can believe them or not, just as you choose to believe them when I am speaking to you in an informal or formal setting.

But unlike these other forms of transient communication, where my words evaporate into the air, blogs live on the net. They are searched by Google, so they can be found easily. And they are living things, open to comment, discussion, updating. Once I realized what a blog could be, I could fire one off in a matter of minutes. Do I get some things wrong? Sure. But isn’t that why we communicate with each other in science, so we can try to put our thoughts in order in a way where flaws can be exposed? It was a magical moment when I read over a blog that I had posted earlier and realized that I had left out a part of the argument. Oh no! But then I just opened edit and put it in. But what if I misrepresent some part of an argument or forget to acknowledge someone? Isn’t that why we have peer review? Well, if you want peer review, just read the comments. Usually, someone will correct you if they care enough. And again, you can immediately acknowledge that input and modify your posting or post a new one. So rather than blogging taking me away from my job, I actually think it lets me do it better. It is a freeing form of communication. Scientists generally are interesting people, but you would never know it from the articles they produce. But you do when you get them talking. And that, imho, is what a blog should be: scientists talking for everyone’s benefit.

by Anita Bandrowski

Dr. Landis, and the rest of the ‘who-is-who-in-science’ have recently published a paper (PMID:23060188) in Nature about the reporting practices in biological sciences. This follows some of the reports that have ruffled the scientific community recently, such as the study by Amgen scientists (PMID:22460880), which reported that less then 10% of major cancer studies were replicable. Now, however you may feel about Amgen and the rest of the biotech industry, what is the point of publishing research that can’t be replicated? Are we, as a community, falling down on the job? We are paid to do research, train students in the scientific method and publish that research. We are the wise old men (and women) who should hold the line against the fast, the easy and the popular. Instead, we as a community are falling into various pitfalls that we ought not to fall into. Indeed, one satirical statistician pointed out (repeatedly, but apparently Amgen and others have yet to listen) that just about every report in one of the top tier journals is an anomaly (PMC1182327). We could perhaps pause, and think about this.

The issues that were brought up by Dr. Landis sound like what my advisor was trying for years to beat into my head many many years ago when I was a young and naive graduate student.

1. Report how you randomized the study.

2. Blind study design is better than not blind.

3. Estimate sample size by using an actual formula (its easy just manipulate the t-test formula to solve for n).

4. Tell us (or better still show us) what you have done with data (if you used statistical software, which one, which version, which machines).

Why does a director of the NIH have to tell the scientific community this? Is this no longer taught in graduate school? I am not sure how many other people have had weeks of experimental findings thrown (when data was still on paper) into the trash due to inadequate controls, but seems like perhaps it should be done a lot more often.

I am certainly no expert on teaching or training, but interacting with some great teachers I have learned that “students will always hate advisors, its just a matter of when” (Glenn Hatton, ~1999). In my case, this happened when my paper was returned marked up stating something to the effect of: “provide softer toilet paper next time.” Although I hated my advisor at the time, I really wish I had kept that gem.

Perhaps as a community, we could rethink the incentive structure in biology because papers that are reasoned, well controlled, thorough and meticulous are seldom published in very high impact journals because they are not sufficiently novel or surprising. We hire scientists based on having published in one of the ‘novelty seeking’ journals. Grants are often penalized because they are not sufficiently novel or exciting. Meaning that, careful reasoned research is being penalized and seeking novelty is rewarded? Would Darwin have gotten funding from NIH or would it not be sufficiently novel to measure beak size?

Is this the way that science ought to be incentivized?