Dear UCLA IMED Seminar SPAM – I will NOT maintain your emails in a safe, secure and confidential manner

Grr.

I have gotten a few email announcements – that I did not sign up for – from a seminar series from UCLA called IMED.  The emails come with a warning at the end:

IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.

No – I will not keep your emails in a safe, secure and confidential manner.  No way to unsubscribe from the emails.  I did not sign up for them.  This is SPAM.  And even if it was not SPAM I would certainly not follow such a warning.  Am wondering – do these warning EVER hold any legal authority?

1/22 at #UCDavis Provost’s Forum on Access and Affordability

Just received this announcement for what seems to be an interesting talk tomorrow …

Dear UC Davis Faculty, Staff, Students and Community Members,

We are pleased to announce that the next event in the Provost’s Forums on the Public University and the Social Good will be held tomorrow on Wednesday, January 22nd.

UC Davis Professor Ann Huff Stevens, Chair of the Study Group on Accessibility and Affordability, Professor and Chair of Economics and Director of the Center for Poverty Research, along with a panel of UC Davis undergraduate students will discuss on the topic of “Access and Affordability: Student and Faculty Perspectives.”

Professor Stevens will present the findings of the Study Group on Accessibility and Affordability, a group created to evaluate and develop ideas, strategies, and programs to help the campus achieve the UC Davis vision of maintaining and expanding access to an excellent undergraduate education. Professor Stevens’ presentation will be followed by a panel of undergraduate students discussing their experiences and observations on these issues, as well as a question and answer session with the students and Professor Stevens.

The event will begin in Memorial Union Room II at 4:30 p.m. and will conclude at 6:30 p.m. after a reception with light refreshments. We hope to see you at this exciting event!

For more details of this event please see the attached event program, visit our website: The Provost’s Forums on the Public University and the Social Good, or contact Casey Castaldi. In addition, please forward to any interested parties, as all events are open to the public.

1.22.14 Program.pdf

Overselling the microbiome story of the week: aging in fruit flies vs humans

Well, I like fruit flies too.  But the claims in this story are quite a jump: Gut bacteria health may be the key to living longer, disease-free lives, U.S. fruit fly study reveals | National Post.

Some choice quotes:

Researchers have more than just a gut feeling they’ve discovered one of the keys to living a longer, healthier life, especially as we age.

Emphasis on we by me.  Jumps right in there and basically says this study is about people even though it is not.

But this research goes further, study authors said, putting gut bacteria shifts “into a hierarchical, causal relationship and highlights the points where we can intervene.”

Where we can intervene in all the premature aging that happens in the fruit flies in our houses.

“If we can understand how aging affects our commensal population (the bacteria that live inside us) — first in the fly and then in humans — our data suggest we should be able to impact health span and life span quite strongly,” Jasper said. “Because it is the management of the commensal population that is critical to the health of the organism.”

How does Jasper go from their fruit fly study to “we should be able to impact health span and life span quite strongly.”???????  Again, I love fruit flies.  And I love their microbiome.  I think that Drosophila is a great model system for studying animal microbiomes.  I have even coauthored a few papers on Drosophila and the microbes that live in and on it.  Examples include

But let’s not get ahead of ourselves in the implications of this work for humans.

Pubchase recommended papers to read system pretty good …

Been playing around with Pubchase for various reasons and I have discovered that their system for recommending papers to read is quite good.  What I first did was try to upload my reference collection to Pubchase (I think it did not quite finish but most of the papers I have in my collections got in there).  And then I played around with Pubchase a bit.  And I got busy as usual.  And then I was pleasantly surprised to get an email with recommended papers to read / add to my collection.

Below I have posted the list from the latest email.  The recommendations are spot on.  The links take you to a Pubchase page for each paper and if you have an account there you can add them to ones collection or go directly to the paper.  Definitely worth checking out ..

Jan 10, 2014 International Journal Of Systematic And Evolutionary Microbiology
Kosowski K, Schmidt M, Pukall R, Hause G, Kämpfer P, Lechner U
Jan 06, 2014 Molecular Biology And Evolution
Zhong B, Xi Z, Goremykin VV, Fong R, McLenachan PA, Novis PM, Davis CC, Penny D
Jan 13, 2014 World Journal Of Microbiology & Biotechnology
Blöchl E, Burggraf S, Fiala G, Lauerer G, Huber G, Huber R, Rachel R, Segerer A, Stetter KO, Völkl P

The family name Solimonadaceae Losey et al. 2013 is illegitimate, proposals to create the names ‘Sinobacter soli’ comb. nov. and ‘Sinobacter variicoloris’ contravene the Code, the family name Xanthomonadaceae Saddler and Bradbury 2005 and the order name Xanthomonadales Saddler and Bradbury 2005 are illegitimate and notes on the application of the family names Solibacteraceae Zhou et al. 2008, Nevskiaceae Henrici and Johnson 1935 (Approved Lists 1980) and Lysobacteraceae Christensen and Cook 1978 (Approved Lists 1980) and order name Lysobacteriales Christensen and Cook 1978 (Approved Lists 1980) with respect to the classification of the corresponding type genera Solibacter Zhou et al. 2008, Nevskia Famintzin 1892 (Approved Lists 1980) and Lysobacter Christensen and Cook 1978 (Approved Lists 1980) and importance of accurately expressing the link between a taxonomic name, its authors and the corresponding description/circumscription/emendation.
Jan 10, 2014 International Journal Of Systematic And Evolutionary Microbiology
Tindall BJ
Jan 10, 2014 International Journal Of Systematic And Evolutionary Microbiology
Tindall BJ
Jan 10, 2014 International Journal Of Systematic And Evolutionary Microbiology
Kwon T, Baek K, Lee K, Kang I, Cho JC
Jan 17, 2014 GigaScience
Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou WC, Corbeil J, Del Fabbro C, Docking TR, Durbin R, Earl D, Emrich S, Fedotov P, Fonseca NA, Ganapathy G, Gibbs RA, Gnerre S, Godzaridis E, Goldstein S, Haimel M, Hall G, Haussler D, Hiatt JB, Ho IY, Howard J, Hunt M, Jackman SD, Jaffe DB, Jarvis ED, Jiang H, Kazakov S, Kersey PJ, Kitzman JO, Knight JR, Koren S, Lam TW, Lavenier D, Laviolette F, Li Y, Li Z, Liu B, Liu Y, Luo R, Maccallum I, Macmanes MD, Maillet N, Melnikov S, Naquin D, Ning Z, Otto TD, Paten B, Paulo OS, Phillippy AM, Pina-Martins F, Place M, Przybylski D, Qin X, Qu C, Ribeiro FJ, Richards S, Rokhsar DS, Ruby JG, Scalabrin S, Schatz MC, Schwartz DC, Sergushichev A, Sharpe T, Shaw TI, Shendure J, Shi Y, Simpson JT, Song H, Tsarev F, Vezzi F, Vicedomini R, Vieira BM, Wang J, Worley KC, Yin S, Yiu SM, Yuan J, Zhang G, Zhang H, Zhou S, Korf IF
Jan 17, 2014 Nature Reviews. Genetics
Sims D, Sudbery I, Ilott NE, Heger A, Ponting CP
Jan 10, 2014 International Journal Of Systematic And Evolutionary Microbiology
Amouric A, Liebgott PP, Joseph M, Brochier-Armanet C, Lorquin J
Jan 07, 2014 Cancer Research
Bajrami I, Frankum JR, Konde A, Miller RE, Rehman FL, Brough R, Campbell J, Sims D, Rafiq R, Hooper S, Chen L, Kozarewa I, Assiotis I, Fenwick K, Natrajan R, Lord CJ, Ashworth A
Jan 15, 2014 BioEssays : News And Reviews In Molecular, Cellular And Developmental Biology
List JM, Nelson-Sathi S, Geisler H, Martin W
Jan 08, 2014 Proceedings Of The National Academy Of Sciences Of The United States Of America
Marino S, Baxter NT, Huffnagle GB, Petrosino JF, Schloss PD
Jan 06, 2014 FEMS Microbiology Reviews
Boon E, Meehan CJ, Whidden C, Wong DH, Langille MG, Beiko RG
Jan 15, 2014 World Journal Of Microbiology & Biotechnology
Tindall BJ
Jan 10, 2014 Indoor Air
Araki A, Saito I, Kanazawa A, Morimoto K, Nakayama K, Shibata E, Tanaka M, Takigawa T, Yoshimura T, Chikara H, Saijo Y, Kishi R
Jan 17, 2014 Astrobiology
La Duc MT, Venkateswaran K, Conley CA
Jan 16, 2014 Nature
Roy MG, Livraghi-Butrico A, Fletcher AA, McElwee MM, Evans SE, Boerner RM, Alexander SN, Bellinghausen LK, Song AS, Petrova YM, Tuvim MJ, Adachi R, Romo I, Bordt AS, Bowden MG, Sisson JH, Woodruff PG, Thornton DJ, Rousseau K, De la Garza MM, Moghaddam SJ, Karmouty-Quintana H, Blackburn MR, Drouin SM, Davis CW, Terrell KA, Grubb BR, O’Neal WK, Flores SC, Cota-Gomez A, Lozupone CA, Donnelly JM, Watson AM, Hennessy CE, Keith RC, Yang IV, Barthel L, Henson PM, Janssen WJ, Schwartz DA, Boucher RC, Dickey BF, Evans CM
Jan 06, 2014 Frontiers In Microbiology
Rodionova IA, Li X, Thiel V, Stolyar S, Stanton K, Fredrickson JK, Bryant DA, Osterman AL, Best AA, Rodionov DA
Jan 17, 2014 Applied And Environmental Microbiology
Porras-Alfaro A, Liu KL, Kuske CR, Xie G
Jan 17, 2014 Molecular Ecology
Primmer CR, Papakostas S, Leder EH, Davis MJ, Ragan MA
Jan 17, 2014 Astrobiology
Venkateswaran K, Vaishampayan P, Benardini JN, Rooney AP, Spry JA
Jan 17, 2014 Applied And Environmental Microbiology
Toenshoff ER, Szabó G, Gruber D, Horn M
Jan 15, 2014 Clinical Microbiology And Infection : The Official Publication Of The European Society Of Clinical Microbiology And Infectious Diseases
Bichaud L, Izri A, de Lamballerie X, Moureau G, Charrel RN
Jan 16, 2014 American Journal Of Respiratory And Critical Care Medicine
Depner M, Fuchs O, Genuneit J, Karvonen AM, Hyvärinen A, Kaulek V, Roduit C, Weber J, Schaub B, Lauener R, Kabesch M, Pfefferle PI, Frey U, Pekkanen J, Dalphin JC, Riedler J, Braun-Fahrländer C, von Mutius E, Ege MJ, PASTURE Study Group
Jan 10, 2014 PLoS Biology
Eisen JA, Ganley E, Maccallum CJ
Jan 16, 2014 Bioinformatics (Oxford, England)
Matias Rodrigues JF, von Mering C
Jan 08, 2014 Environmental Health : A Global Access Science Source
Casas L, Tischer C, Wouters IM, Torrent M, Gehring U, Garcia-Esteban R, Thiering E, Postma DS, de Jongste J, Smit HA, Borràs-Santos A, Zock JP, Hyvärinen A, Heinrich J, Sunyer J
Jan 07, 2014 BMC Bioinformatics
Roberts A, Feng H, Pachter L
Jan 17, 2014 Astrobiology
Benardini JN, La Duc MT, Beaudet RA, Koukol R
Jan 17, 2014 Astrobiology
Benardini JN, La Duc MT, Ballou D, Koukol R
Jan 10, 2014 Science (New York, N.Y.)
Biller SJ, Schubotz F, Roggensack SE, Thompson AW, Summons RE, Chisholm SW
Jan 08, 2014 Proceedings Of The National Academy Of Sciences Of The United States Of America
Bokulich NA, Thorngate JH, Richardson PM, Mills DA
Jan 17, 2014 Genome Biology And Evolution
Oakeson KF, Gil R, Clayton AL, Dunn DM, von Niederhausern AC, Hamil C, Aoyagi A, Duval B, Baca A, Silva FJ, Vallier A, Jackson DG, Latorre A, Weiss RB, Heddi A, Moya A, Dale C
Jan 06, 2014 PloS One
Ghosh TS, Gupta SS, Nair GB, Mande SS
Jan 13, 2014 PLoS Genetics
Wang D, Ning K, Li J, Hu J, Han D, Wang H, Zeng X, Jing X, Zhou Q, Su X, Chang X, Wang A, Wang W, Jia J, Wei L, Xin Y, Qiao Y, Huang R, Chen J, Han B, Yoon K, Hill RT, Zohar Y, Chen F, Hu Q, Xu J
Jan 06, 2014 BMC Genomics
Thompson CC, Chimetto L, Edwards RA, Swings J, Stackebrandt E, Thompson FL
Jan 10, 2014 Planta
Ogawa T, Ishikawa H, Shimada K, Shibata K
Jan 09, 2014 International Journal Of Molecular Sciences
Zan J, Liu Y, Fuqua C, Hill RT
Jan 15, 2014 Proceedings Of The National Academy Of Sciences Of The United States Of America
Wales DJ, Salamon P
Jan 17, 2014 Molecular Phylogenetics And Evolution
Smith DR, Arrigo KR, Alderkamp AC, Allen AE
Jan 13, 2014 PloS One
Finucane MM, Sharpton TJ, Laurent TJ, Pollard KS
Jan 09, 2014 BMC Genomics
Benedict MN, Henriksen JR, Metcalf WW, Whitaker RJ, Price ND
Jan 08, 2014 Frontiers In Microbiology
Labonté JM, Suttle CA
Jan 13, 2014 PloS One
Fagen JR, Leonard MT, McCullough CM, Edirisinghe JN, Henry CS, Davis MJ, Triplett EW
Jan 13, 2014 PloS One
Kienesberger S, Sprenger H, Wolfgruber S, Halwachs B, Thallinger GG, Perez-Perez GI, Blaser MJ, Zechner EL, Gorkiewicz G
Jan 07, 2014 Environmental Science & Technology
Kulp TR, Miller LG, Braiotta F, Webb SM, Kocar BD, Blum JS, Oremland RS
Jan 07, 2014 Journal Of Proteome Research
Higdon R, Stewart E, Stanberry L, Haynes W, Choiniere J, Montague E, Anderson N, Yandl G, Janko I, Broomall W, Fishilevich S, Lancet D, Kolker N, Kolker E
Jan 17, 2014 Planta
Brandt P
Jan 15, 2014 Planta
Brandt P
Jan 14, 2014 World Journal Of Microbiology & Biotechnology
Yuan P, Ogawa A, Ramamurthy T, Nair GB, Shimada T, Shinoda S, Takeda T

EVE faculty candidate at #UCDavis Barbara Fernandez-Going 1/21 Do soil type and spatial heterogeneity buffer competing species against climate change?

DEPARTMENT OF EVOLUTION AND ECOLOGY

RECRUITMENT SEMINAR

ECOLOGIST

Dr. Barbara Fernandez-Going

Postdoctoral Researcher

University of California, Santa Barbara and

Utah State University

“Do soil type and spatial heterogeneity buffer competing species against climate change?”

Tuesday, January 21st, 2014

4:10pm

1022 Life Sciences Building

Faculty Host: Professor Don Strong, Department of Evolution and Ecology

This looks awesome: DC Art Science Evening Rendezvous (DASER) 2/20

Wow – this looks awesome.  Bummed I can’t be there — DC Art Science Evening Rendezvous (DASER)

From their web site:

DC Art Science Evening Rendezvous (DASER)
Thursday, February 20, 2014, 6 p.m. (doors open at 5:30)
Keck Center, 500 Fifth St., N.W., Room 100

Free and open to the public. Registration and photo ID required.

Email cpnas@nas.edu by February 6, 2014 to request American Sign Language interpretation.

D.C. Art Science Evening Rendezvous (DASER) is a monthly discussion forum on art and science projects in the national capital region and beyond. DASERs provide a snapshot of the cultural environment and foster interdisciplinary networking. This month, in celebration of its third anniversary, DASER explores the theme of art as a way of knowing. Access the live webcast. It begins streaming at 5:30 p.m. EST.

5:30 to 6:05 p.m. Welcoming remarks

6:05 to 6:10 p.m. Community sharing time. Anyone in the audience currently working within the intersections of art and science will have 30 seconds to share their work. Please present your work as a teaser so that those who are interested can seek you out during social time following the event.

6:10 to 7:10 p.m. Panelists’ presentations (15 minutes each)

Michele Banks, Artist, Washington, D.C.
Diane Burko, Artist, Philadelphia, Pennsylvania
Robert Root-Bernstein, Professor of Physiology and Bioartist, Michigan State University, East Lansing
Nina Samuel, Art and Science Historian and Independent Curator, New York City and Berlin, Germany

7:10 to 8:00 p.m. Discussion

8:00 to 9:00 p.m. Reception

DASER is co-sponsored by Cultural Programs of the National Academy of Sciences (CPNAS) and Leonardo, the International Society for the Arts, Sciences, and Technology. DASER fosters community and discussion around the intersection of art and science. The thoughts and opinions expressed in the DASER events are those of the panelists and speakers and do not necessarily reflect the positions of the National Academy of Sciences or of Leonardo.

Seminar 1/21 at #UCDavis: Melanie Gareau Gut Feelings: How intestinal microbes influence the brain

DEPARTMENT OF NEUROBIOLOGY, PHYSIOLOGY & BEHAVIOR

PHYSIOLOGIST RECRUITMENT SEMINAR

Melanie Gareau

Assistant Adjunct Professor

School of Medicine

University of California, San Diego

"Gut Feelings: How intestinal microbes influence the brain"

Tuesday, January 21, 2014

9:00am

1022 Life Sciences Building

Melanie Gareau Seminar Flyer.doc

Deep Thoughts by Bill Keller Volume 2: Heroic Wheels of Science

UPDATE 1/25: (Since some people asked / were confused) — Wrote this to get people to think about how ridiculous the article by Bill Keller was in the New York Times about Lisa Adams.  I took his article about Lisa Adams and edited it to be about Stephen Hawking.  I don’t think there is any chance in hell the New York Times would have let him publish this – because it is about Hawking and because Hawking is famous and – well – possibly because Hawking is a man.  Anyway – I think Keller and his wife should be thoroughly lambasted in the press continuously for what they did and this is my contribution I guess.

——————————————————————-

From Bill Keller *

For those of you who saw my article about Lisa Adams in the New York Times on January 12, you should know that I have some very very deep thoughts I would like to share with others about how people communicate on social media about their medical problems.  I note – for those critics out there you should check out the completely and thoroughly independent assessment by Emma Keller.  Though I am married to Emma, we never actually communicate about anything (I think she may hate me) so her piece is independent.  Proof that her piece was brilliant is that the Guardian, a corrupt newspaper if I have ever seen one, removed it claiming “policy violations.”  Anywoo – because I am completely confident in the righteousness of my article (despite the vitriolic and over the top wasteful criticism of it from places like Slate, NPR, The Nation, Salon, the Washington Post, and more), and because the world clearly needs me to write more about this, I am starting a new series here.  I call it Deep Thoughts by Bill Keller.  Today’s article is below.


Heroic Wheels of Science

STEVEN HAWKING has spent the last 40+ years in a fierce and very public cage fight with death. Since a diagnosis of motor neuron disease detected the first toxic seeds of amyotrophic lateral sclerosis in his body when he was 21, he has continued to carry out scientific research and appear in public even with the advancing disease. He has written dozens of papers and books and travelled around the world discussion science through all the medical treatments. Even by contemporary standards of scientific work by people will illnesses, he is a phenomenon. (Last week he was involved in an announcement of a professorship at Cambridge University that is named after him – how arrogant.) A rapt audience of 200,000 thousand followers on Twitter and 222,000 on Facebook follow his every move – including lots of detail about space-time, about the universe, and even occasionally about his problems with ALS and his wheelchair along with all the news stories about his slow slide into death.

In the last few year, his writings have changed tone slightly; his optimism about understanding the universe and his own role in it has become a little less unassailable As 2013 ended, the ALS that had damaged his nervous system had continued to progress. He was deemed too sick to travel to some award ceremonies and conferences. He continues to be wheelchair bound and the ALS research community has embraced him as a model subject and proselytizer for medical research.

Steven Hawking is still alive, still doing research, and insists he is not dying, but the news about him has become less about prolonging his survival and more about managing his deteriorating health. His research and commentary has become darker (e.g., he focuses now on “dark” matter and God – clearly showing he is spiraling into depression). “The missing link in cosmology is the nature of dark matter and dark energy” he “said” the other day at Caltech (I note – I use the quotes for said because I am not sure whether he actually should be considered speaking).

As many who read my brilliant work know, my father-in-law’s died from cancer in a British hospital.  There were people in the hospital with ALS.  Therefore, I am an expert in ALS.  Plus,there were lots of physicians at the hospital and I talked to them a lot so I am also perfectly capable of commenting on physics now.

Among doctors here in the pathetic United States, there is a growing appreciation of palliative care for ALS patients that favors the quality of the remaining life rather than endless “heroic measures” that may or may not prolong life but assure the final days are clamorous, tense and painful. (And they often leave survivors bankrupt – although apparently Hawking has some money.) What Britain and other countries know, and my country (I refer to the US as my country because I am actually the leader of this country) is learning, is that every ALS patient need not be Hastings, a war of attrition waged regardless of the cost or the casualties. It seemed to me, and still does, that there is something enviable about going just getting it the fuck over and dying quickly. One intriguing study even suggests (although it is so important that I refuse to link to it here) that ALS patients given early palliative care instead of the most aggressive ALS therapy not only have a better quality of life, they actually live a bit longer.

When my wife, the brilliant and insightful Emma (who was named after the wonderful Emma from the Jane Austen book) thought about writing about Hawking for that crappy paper The Guardian, she introduced me to Hawking, who I had never heard of.  After this, my first thought was about how brilliant my wife is.  And about how brilliant I am.  And then I thought about food, for I was hungry.  And then I thought about how I used to be famous and worked at the New York Times.  And I was brilliant there.  And then I took a bath.  And then I went for a walk in my very large estate and used my functioning legs and my ALS-free body.  And then I looked at some birds and flowers.  And after  few weeks of this relaxation, I though of my father-in-law’s calm death and the person with ALS who I think was in the hospital and all those physics studying physicians who worked there.  And I thought about how Stephen Hawking’s choice was in a sense the opposite. His aim was to buy as much time as possible to watch his two children (Robert, Lucy and Timothy) grow up and to apparently do some more science although since I don’t understand what he works on I think it is probably not worth it. Anyway he is all about heroic measures. He is constantly engaged in battlefield strategy with his medical team – fighting ALS like some sort of fight. There is always the prospect of another research trial to excite his hopes. He responds defiantly to any suggestion that the end is approaching.

“I am not on my deathbed,” he could have told me in an email from a meeting – if he had bothered to answer the nasty email I sent him suggesting he should just die. “Periods of ALS progression and stability are part of the natural course of this disease. I will be continuing to do science and to talk about my life and diagnosis for some time to come,” he could have predicted if he would have answered me.  And I hope he is right. In any case, I cannot imagine Stephen Hawking reaching a point where resistance gives way to acceptance. That is entirely his choice, and deserving of our respect. But his decision to live his ALS onstage and to have the incredible gall to continue to work invites us to think about it, debate it, learn from it.  Or – at least – that is the justification I have made up in order to write this piece.

The first thing I would say is that his “decision” to treat his terminal disease as a military campaign has worked for him (I note – I put decision in quotes here because apparently my making something up about another person is not actually a decision of their’s — weird). His relationship with his doctor’s and his being famous and all that provides him with intensive, premium medical care, including not just constant maintenance and aggressive treatment but such amenities as a wheelchair that works, a voice synthesizer, help with various activities, and even special parking permits in cities like New York where it is really fucking hard to find parking. (Neither Hawking nor his doctors would tell me what all this costs or whether it is covered by insurance.)

Whether or not this excellent care has added months or years to his life, as he clearly believes, is a medical judgment, and his doctors, bound by privacy rules, won’t say (although I note – I did try to hack into his computer accounts and his email but it turns out I do not know what hacking even means or what a computer account is). Most trials of new drugs aim to determine safety and calibrate dosages, and make no promise of slowing the ALS disease in the participants. I note – that is so asinine – not promising things when one cannot.  But any reader can see that Hawkings online omnipresence has given him a sense of purpose – especially in regard to scientific research – and a measure of control in a tumultuous time, and the comfort of a loyal, protective scientific community who apparently think he is some sort of supergenious. Social media and media coverage has become a kind of self-medication.

Stephen Hawking’s defiance has also been good for physics and the ALS community. He has been an eager science supporter, and those, I was surprised to learn (by a google search), are in short supply. Emma – my brilliant wife – told me of a study showing that only 3 percent of adults believe in science  and an even smaller percent of ALS patients (something like 99%) participate in research trials.  The reluctance of this 1% has been “a huge bottleneck in ALS research.” according to the thing I just typed. Amazingly, some 1 percent of clinical trials aimed to focus on ALS fail to get the minimum enrollment. Hawking has been a cheerleader for ALS research in general and also for physics and science education in general. In fact, he has implored followers to become scientists and also to contribute to ALS research funds in his name.  What a douche. “We love him!” the scientific community would have tweeted if there was a single scientist on Twitter about the Hawking phenomenon. And the ALS community might have said “An important contribution to ALS patients, families, and clinicians! :)”

Beyond that, whether his scientific work has been a public service is a more complicated question since he works on really fucking complicated science.

“I am public about this disease in order to shed light on the daily lives of people living with this diagnosis rather than hiding behind the secret ALS gang party that is the only one that gets the spotlight,” he might have told me in an email – again – if he would frigging answer me. (The ubiquitous references by ALS charities to Lou Gehrig and Hawking have been faulted for making it seem like you should not just die once you get diagnoses with ALS.)

Hawking’s research and digital presence is no doubt a comfort to many of his followers. On the other hand, as ALS experts I consulted pointed out, Hawking is the standard-bearer for an approach to ALS that makes it seem like some people with ALS don’t just die.  And that may raise false hopes, and that, implicitly, seems to peg patients like the person who I thought had ALS at the hospital where my father was as failures (this guy – if he had ALS – never won and honorary PHDs from anywhere – nor did he win any World Series rings).

Steven Badman, an associate dean of the Keller University School of Medicine, said he cringes at the idea that people with ALS can do stuff before they die, because it suggests that those who choose not to spend their final days doing something useful, using every weapon in the high-tech medical arsenal, lack character or willpower.

“I’m the last person to second-guess what he did,” Badman told me, after reading up about Hawking. “I’m sure his work has brought meaning to some trying to understand the universe and to some with ALS – a deserved sense of accomplishment. But it shouldn’t be unduly praised.  After all science is really a waste of time.  As is living.  And since we are all going to die, why not just get on with it.”


* Reports of this not being by Bill Keller are apparently accurate.

rRNA sequencing services – summary of available services

Posted a request to Twitter and microBEnet about rRNA sequencing services.  Here is a Storify of the results

Top alternatives to quilt plots and heat maps

Quilt Plot from PLOS One

If you have missed the uproar over Quilt Plots and whether or not they are Heat Maps, well, you have then missed the uproar over Quilt Plots and whether or not they are Heat Maps.  It has been uproarious.  But you may not know that the literature pre-anticipated this uproar and many already developed alternatives, even if they did not know it.  And here are the top ones.



Guilt plots

In “Prediction of gene function by genome-scale expression analysis: prostate cancer-associated genes” by Walker et al. they report the development of a method “we call Guilt-by-Association (GBA).”  Unfortunately, and amazingly, there are NO FIGURES IN THE PAPER.  Fortunately, lots of other people have done similar GBA methods.  A figure from one such study is below

A Guilt Plot

Alas even though some people now call these Eisengrams, they certainly should have been called Guilt Plots.  And that is what I am renaming them.


Beet maps

Not much to say other than this is simply visionary:

Beet Map


Wheat maps

Jorge Dubcovsky at UC Davis just won the Wolf Prize.  What did he win it for.  Wheat Maps of course.  Like this one from a Genetics paper in 1996.


Seat maps

If only someone had thought to make maps of seating arrangements in different facilities, like stadiums, or planes, they could have been famous.  Oh well.


Meat maps

I love meat maps.  They are just awesome.  And here are a few good ones.  And each should be trademarked in some way

Meat Map from Grist

An App of Course

The Meat Map of the World


Feet maps

OK.  I don’t really know what reflexology is but the “feet maps” here are cool to look at.


Tilt plots

See this one.

Tilt Plot



Wilt Plots

Many different kinds here.  This one is nice

A Wilt Plot


Of course there are so many more maps and plots that are on par with quilt plots that I could go on like forever.  I may post more – stay tuned.  This is just exciting stuff.