Want to learn more about the future of genomics?

My department is hosting a panel on “The Future of Genome Sciences” that is free and open to the public. Here are the details:

Panel Discussion: The Future of Genome Sciences
Monday, May 7th
7:00 pm, Kane Hall EDIT: 120
University of Washington
Seattle, WA
free, no registration required

The speakers will be:

Dr. Bruce Alberts who President Obama has appointed as one of his first Science Envoys.  Dr. Alberts is editor of Sciencemagazine, author of The Cell, and former President of the National Academy of Sciences.

Dr. Natalie Angier who is a science writer for The New York Times and the Andrew D. White Professor-at-Large at Cornell University.  In 1991 she received the Pulitzer Prize for Beat Reporting.

Dr. James Evans who is the Bryson Distinguished Professor of Genetics and Medicine at University of North Carolina and directs the Clinical Cancer Genetics Services at UNC.

Dr. Keith Yamamoto who is Vice Chancellor for Research, Executive Vice Dean of the School of Medicine, and Professor of Cellular and Molecular Pharmacology at the University of California, San Francisco.

The moderator is Dr. Maynard Olson, who is a Professor in the Departments of Genome Sciences and Medicine at the University of Washington and is one of the founders of the Human Genome Project.

If you’re near Seattle, I hope I’ll see you there!

Dear E. O. Wilson: Please retire or stick to ants

Tonight I went to a talk at Seattle Town Hall by E. O. Wilson, one of the most famous evolutionary biologists still alive today. I admit I went for two different reasons. One, Wilson is super famous and also very old, and I wanted a chance to see him speak because another chance might not come. But two, I saw that the topic was how group selection shaped human evolution, and I wanted to see what controversial arguments he would make.

Controversial because Wilson has recently been stirring the pot by trumpeting group selection and saying kin selection has been debunked. I don’t want to rehash the whole event, but Carl Zimmer has a good summary in the New York Times. The basic thing you need to know is that most biologists consider group selection to only occur in very rare and specific circumstances, and that selection usually takes place at the level of the individual or the gene.

But you wouldn’t know that from the talk. Wilson asserted that his controversial Nature paper definitively overturned kin selection theory and that “no one” responded to his critique of kin selection. This set off a red flag in my head, because I definitely remembered reading criticism of the paper at least in the blogosphere. I grabbed my phone and instantly dug up this critique by Jerry Coyne and this one by Richard Dawkins.

But maybe he meant a published critique. So I googled “response to Nowak 2010” and instantly found a list of papers also published in Nature criticizing his paper:

Abbot, P., Abe, J., Alcock, J., Alizon, S., Alpedrinha, J., Andersson, M., Andre, J., van Baalen, M., Balloux, F., Balshine, S., Barton, N., Beukeboom, L., Biernaskie, J., Bilde, T., Borgia, G., Breed, M., Brown, S., Bshary, R., Buckling, A., Burley, N., Burton-Chellew, M., Cant, M., Chapuisat, M., Charnov, E., Clutton-Brock, T., Cockburn, A., Cole, B., Colegrave, N., Cosmides, L., Couzin, I., Coyne, J., Creel, S., Crespi, B., Curry, R., Dall, S., Day, T., Dickinson, J., Dugatkin, L., Mouden, C., Emlen, S., Evans, J., Ferriere, R., Field, J., Foitzik, S., Foster, K., Foster, W., Fox, C., Gadau, J., Gandon, S., Gardner, A., Gardner, M., Getty, T., Goodisman, M., Grafen, A., Grosberg, R., Grozinger, C., Gouyon, P., Gwynne, D., Harvey, P., Hatchwell, B., Heinze, J., Helantera, H., Helms, K., Hill, K., Jiricny, N., Johnstone, R., Kacelnik, A., Kiers, E., Kokko, H., Komdeur, J., Korb, J., Kronauer, D., Kümmerli, R., Lehmann, L., Linksvayer, T., Lion, S., Lyon, B., Marshall, J., McElreath, R., Michalakis, Y., Michod, R., Mock, D., Monnin, T., Montgomerie, R., Moore, A., Mueller, U., Noë, R., Okasha, S., Pamilo, P., Parker, G., Pedersen, J., Pen, I., Pfennig, D., Queller, D., Rankin, D., Reece, S., Reeve, H., Reuter, M., Roberts, G., Robson, S., Roze, D., Rousset, F., Rueppell, O., Sachs, J., Santorelli, L., Schmid-Hempel, P., Schwarz, M., Scott-Phillips, T., Shellmann-Sherman, J., Sherman, P., Shuker, D., Smith, J., Spagna, J., Strassmann, B., Suarez, A., Sundström, L., Taborsky, M., Taylor, P., Thompson, G., Tooby, J., Tsutsui, N., Tsuji, K., Turillazzi, S., Úbeda, F., Vargo, E., Voelkl, B., Wenseleers, T., West, S., West-Eberhard, M., Westneat, D., Wiernasz, D., Wild, G., Wrangham, R., Young, A., Zeh, D., Zeh, J., & Zink, A. (2011). Inclusive fitness theory and eusocialityNature, 471 (7339) DOI: 10.1038/nature09831

Boomsma, J., Beekman, M., Cornwallis, C., Griffin, A., Holman, L., Hughes, W., Keller, L., Oldroyd, B., & Ratnieks, F. (2011). Only full-sibling families evolved eusociality Nature, 471 (7339) DOI: 10.1038/nature09832

Strassmann, J., Page, R., Robinson, G., & Seeley, T. (2011). Kin selection and eusociality Nature, 471 (7339) DOI:10.1038/nature09833

Ferriere, R., & Michod, R. (2011). Inclusive fitness in evolution Nature, 471 (7339) DOI: 10.1038/nature09834

Herre, E., & Wcislo, W. (2011). In defence of inclusive fitness theory Nature, 471 (7339) DOI:10.1038/nature09835

Yeah, and he said “no one” responded. And it’s not just that Wilson is out of the loop – he came off as being purposefully disingenuous. Not only did he publish a response to the responses (Nowak, M., Tarnita, C., & Wilson, E. (2011). Nowak et al. reply Nature, 471 (7339) DOI: 10.1038/nature09836), but during the Q&A he changed his story and said that people did respond but they were 1. Wrong and 2. In the minority. Even though 1. He never explained why their critiques were incorrect and 2. The vast majority of biologists disagree with his views of group selection and the authors of the critiques weren’t random nobodies; they were very important and accomplished researchers.

I want to give Wilson the benefit of the doubt. Maybe when he said “no one responded” he meant “no one responded in a way that we think invalidates our hypothesis.” But even then, the rest of his talk was incredibly sloppy. He asserted that human eusociality evolved via group selection, but didn’t offer a shred of evidence the whole time. No proposed mechanism, no genetic evidence, nothing. He just waved the Wand of Group Selection and asserted it happened. He asserted that humans first ate cooked meat by scavenging carcasses from wildfires. That’s one hypothesis among many, but he presented it as a known truth and gave no evidence or citation for it. He asserted that eusociality only evolved recently but again gave absolutely no evidence as to why he thought so. I mean, maybe he’s right, but eusociality isn’t exactly something that fossilizes well, so it could have possibly existed in past species. At least put some sort of qualifier or explanation of your reasoning out there.

When someone in the Q&A asked him to explain why people disagree with group selection so much, he didn’t explain the objections or why he thinks kin selection was wrong. He instead stated that his paper was reviewed by a mathematician from Harvard and that it got into the prestigious journal Nature. Therefore it is right, or something. Here’s an alternative hypothesis: Your paper got published in Nature because you’re insanely famous and it was incredibly controversial, which Nature eats up. Nature is more about prestige and sexy topics than good science nowadays. Its retraction rate has increased ten fold in the last ten years when the number of papers published in all journals has only increased by 44%.

Look, I’m not a priori against group selection. Maybe Wilson is right and group selection is applicable in more situations that we currently think. But I’m not going to accept it until he presents compelling evidence, which he utterly failed to do. You can’t just say “Harvard” and “Nature” and leave it at that.

The most irritating thing about the night was that this was a talk given to an educated general public. These people are smart enough to appreciate science and know Wilson is a famous scientist, so they’re going to believe whatever he says. On the way out people were raving about how interesting the talk was. But he presented none of the controversy, no evidence, no reasoning, no citations, no qualifiers…nothing. I understand that a talk to the general public isn’t going to get into extreme detail, but asserting your incredibly controversial ideas as scientific fact is incredibly dangerous. This talk reminded me more of stuff I’ve seen from creationists and climate denialists than scientists.

Honestly, I left feeling bad for him. E. O. Wilson made huge advances to evolutionary biology, sociobiology, and conservation. “Huge advances” is an understatement. But tonight he went outside his expertise and left science behind, and it was kind of embarrassing. I would have loved for him to give an hour long talk about ants instead.

Gender Salary Equity in Higher Education

I’m an active member of Women in Genome Sciences, a group in my department that works to make our field more accepting and welcoming to minorities. Today in belated honor of Equal Pay Day we hosted Dr. Laura Meyers who did research here at the University of Washington on the gender pay gap in higher education. I figured it was a topic my readers would be interested in, so here’s a summary of her talk:

Even though the Equal Pay Act and the Civil Rights Act were passed over 40 years ago, female faculty still make less. The average salary in 2009-2010 for men was $80,885, while for women it was $66,653. Dr. Meyers wanted to investigate potential causes of such a pay gap, like:

  • Segregation of women to lower paying jobs/fields (Education field is predominantly female and not well paid)
  • Nonmarket responsibilities as mothers/caregivers
  • Higher attrition rates in tenure-track positions
  • Devaluation of women’s work. Women are more likely to have  more teaching and service tasks (being on committees, running events and seminars, participating in outreach). However, research gets paid better than teaching or service
  • Lack of training and on-the-job education
  • Salary negotiation – are women not as good at it for whatever reason?
  • Organization behaviors and equity/salary/promotion policies

Her work takes three main categories of variables into account:

  1. Gender (Your gender and the percentage of your field that’s female)
  2. Human capital (Amount of training, rank, tenure status)
  3. Structural effects (Average faculty class loads, percent of faculty with funded research, average number of publications)

What is the effect of gender on things like base faculty salary, base faculty salary by discipline type, and base faculty salary by institution type? What is the effect of being in a female dominated or male dominated field? To answer these questions, she used the 2004 National Study of Postsecondary Faculty, the most comprehensive survey of faculty out there. It includes 11,257 Faculty affiliated with 26 disciplines and 860 institutions. The downside is that it’s a single snapshot of time and from 8 years ago, but it’s really the best data we have.

Her major findings were:

  • When looking at gender alone, there is a 14.3% gender salary gap. This is reduced to a 4.8% gap when you take the other variables into account. The variable that had the most effect on reducing the gap was rank and status. This is because there’s a high attrition rate for women in tenure track positions, especially in STEM fields, mostly due to policy and climate. So professors who are farther along in their careers and have tenure get paid better, but there aren’t as many women in these positions.
  • Controlling for other variables, the gender salary gap increases as you move toward institutions that offer higher levels of degrees. Associate’s programs are the most equal, followed by Baccalaureate, then Master’s, with Doctoral institutions being the worst with a 5.7% gap.
  • The gender gap is larger in research based positions than in teaching or service positions. Male faculty receive a larger benefit by focusing on research instead of teaching.
  • A higher proportion of female faculty in a discipline is associated with lower overall faculty salaries in that discipline
  • The gender salary gap is larger in institutions with less female faculty than in institutions with more female faculty. This results in male faculty benefitting financially by working in institutions with less female faculty, but females benefitting financially by working in institution with more female faculty

Dr. Meyers made the following suggestions on how we can combat this remaining pay gap:

  • Have flexible tenure/promotion policies and encourage/require faculty to take advantage of them. Often times alternative policies are in place, but there’s social pressure to not take them.
  • Recognize and reward alternative/varied ways that faculty contribute to a department institution. Women tend to do teaching and service more, and these are often seen as less important as research
  • Female faculty should focus on research that is aligned with mission/goals and tenure/promotion policies of their department. If your department is focused on research, limit service and teaching responsibilities. This is especially true when women are basically guilted onto being on every committee or every outreach event because they’re effectively the token minority. Feel safe in saying “No.”

A professor from my department asked if having publicly available salary data makes a difference. Are women more likely to ask for raises if they know what other people in their department are making? Dr. Meyers said she didn’t know for sure because no research has been done looking at that specifically, but she guessed having that knowledge would help. Someone floated the idea of making this gender gap data publicly available so people could see which institutions suck and with the hopes of the public shame changing things. Dr. Meyers responded that research institutions were the biggest offenders when it came to the pay gap, so you’d have to some how tie it into them receiving grant money for them to care.

Another academic accomplishment!

A new paper that I’m an author on has just been published in DNA and Cell Biology!

It’s a slightly atypical paper, though. When I was a senior undergraduate at Purdue, the Department of Biology staff nominated me to help develop the curriculum of a new NSF-funded, research-based, freshman honors biology laboratory course called CASPiE (Center for Authentic Science Practice in Education). That description is a mouth-full, but it basically means these freshman Biology majors were doing real research for a semester, instead of your typical cookbook lab experiments where the outcome is already known. The class was taught by a professor, a graduate student, and me. I like to say that my main duty was making sure the students plated their bacteria on the correct media and didn’t set themselves on fire*, but I also got to give a lecture on evolution and help out with general concepts throughout the semester.

And now that research has been published in a special undergraduate research edition of the journal DNA and Cell Biology. And it’s atypical because the subject matter is vastly outside of my normal field and interests: Isolation and Preliminary Characterization of Amino Acid Substitution Mutations That Increase the Activity of the Osmoregulated ProP Protein of Salmonella Enterica Serovar Typhimurium. That is going to look bizarrely random on my CV.

But the main congratulations go to the undergrads. They’d be juniors now, and having a paper published by then in a major accomplishment. So kudos to them!

*Though one somehow managed to set the rubber tubing connecting to the gas source on fire. I had a moment of “WTF” and then calmly turned the gas off, and the fire went out. Yay lab classes!

*insert academic joy here* :D

This fell into my inbox this morning:

“Congratulations! I am pleased to inform you that you have been selected to receive a 2012 National Science Foundation (NSF) Graduate Research Fellowship Program (GRFP) Fellowship.”

:D :D :D :D

Can’t say anything else. Too busy dancing around the room.

Grad school update

As I’ve been talking with non-academic friends and family, I’ve realized that not many people understand what actually happens in grad school. I also realized that I don’t talk about it a lot on my blog. I guess it’s one of those things where after doing something all day long, I don’t exactly want to come home and write about it. But I’m in an interesting stage of my grad school career, so I thought I’d fill you in.

I’m currently in the second year of my PhD program. PhD programs in the biological sciences are similar but not identical, so what I say here doesn’t necessarily apply to everyone. For example, my program has first year rotations. We spend fall, winter, and spring quarters doing research projects in different labs. This is to give us exposure to different types of research that we may not have experienced before, and to figure out if the personality of the lab is a good fit for us.

And yes, labs have very distinct personalities. Some expect you to be there 9 to 5, others don’t care when or if you’re physically there as long as you get work done. Some PIs (Principal Investigator – the professor who runs the lab) micromanage, others can be impossible to get a hold of. Some labs are close knit and do lots of social activities together, and others are more distant. These are all things you have to take into consideration in addition to the research, because you actually want to be happy for the next four years.

After your rotation, you pick a lab. With programs that don’t do rotations, you join a lab immediately.

In year 2, you’re deciding your thesis project. What the heck are you going to be researching for the next four years? What questions do you want to ask, and how are you going to investigate them? What kind of experiments are you going to do? What’s your backup plan in case everything goes horribly wrong?

For the curious, my thesis topic is the evolution of microRNA in primates. And that’s about all I can say before I publish anything, unfortunately.

The real purpose of the plan is to make sure you have some goals and guidelines and show that you can think scientifically. It’s not necessarily set in stone. If one of your research ideas just isn’t panning out, there’s no point in continuing down that road. On the flip side, if something completely unexpected and awesome pops up, you should definitely pursue it. The plan is flexible.

But again, you need to prove that you can come up with a general plan and think scientifically. The first step is forming a thesis committee. In my department, your committee has three main components:

  1. Your PI, who serves as committee chair. They’re theoretically supposed to act more as a moderator, but some professors have a problem not throwing in their 2 cents (shocking, I know).
  2. Two or more committee members who can give insight into your project. If you’re collaborating with another lab, their PI will usually be on your committee. Otherwise you try to bring in people whose expertise will help with your project. For example, I picked someone who specializes in human population genetics, in human evolution and statistics, and in classical genetics and evolution.
  3. Your Graduate School Representative (GSR). I think this is something fairly unique to the University of Washington. Your GSR is someone outside of your department who’s your advocate and makes sure your exams are conducted fairly. They can be utterly unrelated to your field if your heart desires or if you have a random professor you really like, but many people use their GSR as a way to fill a missing expertise on their committee. For example, I picked someone with a computational background.

I just formed my committee, and my next step is to have my first committee meeting (in a couple of weeks, gah). The point of committee meetings is to give an update on what you’ve done so far and what you plan to do, and for your committee to give criticism and guidance. The first committee meeting is basically a “This is what I plan to do for my thesis” overview, and your committee sends you off with 438294742 questions about your plan that you need to figure out before your…dun dun dun…General Exam.

In my department, your General Exam is in late May or early July. I like to describe it as the time where people decide whether or not to kick you out of grad school. You get two to three hours to present what you’ve accomplished so far and what you plan to do. Most of the time is spent answering questions from your committee. You’re expected not only to have a solid research plan, but to be extremely familiar with all the prior research and biological concepts relating to your project. It’s basically a 45 minute presentation that’s turned into a 3 hour oral exam. It’s accompanied by a written proposal of your project, but the general consensus is that your committee will read that 30 minutes before you exam (if they read it at all) and it’s not as important. Yes, Professors are procrastinators too.

If you have no clue what you’re talking about, are obviously unprepared, and there’s no hope for improvement, your committee can outright flunk you. You’re done with the graduate program, and if you’ve accomplished enough maybe you can leave with a Master’s degree. This is pretty rare, though. Most of the times you pass, or pass with revisions – you have to edit your written proposal or write extra information about how you’ll deal with your committee’s major concerns.

And then you go drink heavily.

So, if I haven’t been blogging as frequently, or blog even less frequently in the future, that’s why. My first committee meeting is in less than two weeks, and then I’ll be preparing for my General Exam. Which is kind of a Big Deal, in case I didn’t make that clear. I’m especially busy since I’m still trying to do some speaking events, because I’m crazy like that. …And because I can do my work on planes. Hooray for computational work!

Scientific publication title of the day

“Desperately Seeking Stable 50-Year-Old Landscapes with Patches and Long, Wide Corridors” in PLoS Biology.

I’m not sure if the authors purposefully came up with a title reminiscent of a personal ad, or if it’s just my overactive imagination. Either way, it makes me giggle. I mean, “long, wide corridors”? What a size queen.

For anyone wondering what the paper is actually about, the authors are looking for particular types of environments in order to investigate if corridors effectively conserve biodiversity. Human urbanization (roads, housing developments, Walmarts) serves as barriers that plants and animals have a hard time crossing. This fragments large populations into a lot of smaller ones that can’t interbreed as much. Small populations are more susceptible to events that reduce genetic diversity, like inbreeding and genetic drift. Decreasing genetic diversity is generally considered Bad, because…well, I’m lazy and Wikipedia does a good job at explaining:

“Genetic diversity serves as a way for populations to adapt to changing environments. With more variation, it is more likely that some individuals in a population will possess variations of alleles that are suited for the environment. Those individuals are more likely to survive to produce offspring bearing that allele. The population will continue for more generations because of the success of these individuals.”

Corridors are often used to attempt to make up for this fragmentation, and the authors want to see if the corridors are actually successful in promoting gene flow between populations. Thus their personal ad that made me giggle.

More damning revelations about Burzynski’s “research”

Yesterday I picked apart the Burzynski clinic’s list of “scientific studies supporting antineoplason research since 2006.” Unsurprisingly, a majority of these citations were just abstracts of conference presentations lacking peer review, and a couple studies published in terrible (and even sketchy) journals. I wasn’t able to comment on specifics about the papers since I didn’t have access through my university.

A reader sent me a pdf of the first paper from Pediatric Drugs, which is even more incriminating. For one, it’s a review paper. Review papers summarize the current state of scientific knowledge about a certain topic. Sometimes they perform meta analysis on multiple papers, but they don’t always add any new information. Burzynski’s review falls into the latter – that is, it does not have any new peer reviewed data. And the studies about antineoplastons that the paper cites are from multiple conference abstracts, a patent from 1995, his report to the FDA, and an entry in a book by Nova Science Publishers (aka, also all not peer reviewed).

The only peer reviewed research paper the review cites was on the previous list – it was the one published in the crappy alternative medicine journal. I haven’t gotten hold of the paper, but commenter joshtriska summarized it thusly:

[2] A report on 18 patients with “High-Grade, Recurrent, and Progressive Brainstem Glioma” picked from 4 of his clinical trials. The conclusion states that typically less than 10% of patients with this condition survive 2 years, but in his group 22% (or four whole people) survived past 5 years. The conclusion also states that “Because a small number of patients have been evaluated, a larger study is required to confirm these results”. No kidding!

And that final paper – the one published in the sketchy as hell “Cancer Therapy” journal, was also a review:

[3] A review paper, not a study. Antineoplastons are mentioned and a line of data from one of Burzynski’s trials is included in a table. The discussion states that the data concerning antineoplastons was from from conference abstracts, and not peer-reviewed.

The Burzynski clinic is claiming that it’s libelous to say “There are no scientific studies supporting antineoplaston treatment since 2006.” But it’s not libelous because it is true. Results that lack peer review cannot be said to support something. Abstracts at conferences are not peer reviewed. Review papers do not include new, peer-reviewed data. The only published paper he has itself states that it is inconclusive without a larger study to confirm the results.

Plus, they don’t even understand what the phrase “since 2006” means. It means published starting in 2007. From that alone we throw out the first two papers. You’re left with a review paper that cites conference abstracts, and conference abstracts.

So no, Burzynski clinic. There aren’t any scientific studies supporting antineoplaston treatment since 2006. But there are plenty falsifying it.

A look at the Burzynski clinic’s publications

The Burzynski clinic has responded to the flood of skeptical bloggers with a press release. They’ve apparently fired (in so many words) Marc Stephens for his harassment, yet still plan to send attorneys after UK bloggers. I’m not sure if the targeting of UK bloggers has to do with UK libel laws, or if the Burzynski clinic is oblivious to the dozens of American bloggers also pointing out their harmful pseudoscience.

But the part of the press release that intrigued me was that they finally attempt to give some evidence for all that scientific research Burzynski has to back up his claims. Wow, a list of citations! To a non-scientist, it certainly seems impressive, what with its big words and journal names and such. But as a scientist, I was still skeptical, and decided to do some digging.

Why was I skeptical? Because not all journals are created equal. Lay people know this to an extent. It’s much more prestigious to get into journals like Science and Nature because the peer review process is way more rigorous. Your research not only has to be pretty damn air tight, but it has to make a significant contribution to scientific knowledge. We can measure how good a journal is by a metric known as an “impact factor.” It’s complicated, but generally the higher the impact factor, the better the journal.

So let’s have a look at Burzynski’s research, shall we?

1. Burzynski, SR. Treatments for Astrocytic Tumors in Chiìdren: Current and Emerging Strategies. Pediatric Drugs 2006; 8: l67-178.

Pediatric Drugs: No impact factor.

Off to a great start! (Hint: That’s sarcasm)

2. Burzynski, S.R., Janicki, T.J., Weaver, RA., Burzynski, B. Targeted therapy with Antineoplastons A10 and of high grade, recurrent, and progressive breínstem gliome. Integrative Cancer Therapies 2006; 5(1):40­47.

Integrative Cancer Therapies has an impact factor of 1.716. What does this number mean? Compared to other journals in the category of Integrative & Complementary Medicine, it’s ranked 6 out of 21. Not bad, but “Integrative medicine” sets off my Pseudoscience Alarms. Suspicions confirmed, the  journal describes itself as emphasizing “scientific understanding of alternative medicine and traditional medicine therapies.”

To quote the brilliant Tim Minchin:

“By definition … alternative medicine … has either not been proved to work, or has been proved not to work. You know what they call alternative medicine that’s been proved to work? Medicine.”

What happens when you compare this journal in a more legitimate category, like Oncology? Its rank unsurprisingly drops to an abysmal 134 out of 185.

3. Burzynski, SR. Recent clinical trials in diffuse intrinsic brainstem glioma. Cancer Therapy 2007;5, 379-390.

When this journal’s website loaded, I started laughing and dragged my laptop to my fellow-scientist roommate. It looks like a relic from the 90s. Even more sketchy and unprofessional than the white-text-on-black-background and ugly use of frames is its repeated mentioning of its “rapid review process.” I couldn’t find out anything about the editorial board other than there’s some guy in Greece you should submit things to. And after a lot of digging, I couldn’t find an impact factor at all.

Super sketchy.

4. Burzynski, SR., Weaver, R.A., Janicki, T.J., Jufida, G.F., Szymkowskì, B,G., Kubove, E. Phase Il studies of Antineoplasîons A10 and AS 2-1 (ANP) in chiìdren with newly diagnosed diffuse, intrinsic brainstem gliornas. Neuro-Oncology 2007;9:206.

[etc]

The final nine of his citations all seem to come from the Journal of Neuro-Oncology. Upon first glance, it seems legit. It has a relatively high impact factor of 5.483, which makes it 24 out of 184 in Oncology. Not bad at all, especially for a specialized oncology journal (the neuro part).

Not bad until you search the journal for articles by Burzynski. The result?

Burzynski has not published a single paper in this journal. Every single citation is an abstract from a presentation made at a conference. For those of you not in academia, we like to hold conferences where people can present their research and network. However, you’re allowed to present preliminary results that haven’t been published yet. Any scientist can submit abstracts in order to speak at conferences, and if that single paragraph sounds interesting, you get to give a talk. It’s pretty much impossible to judge how legitimate research is from an abstract (or presentation) alone, and some conferences are not competitive at all when it comes to who gets to speak – they have plenty of spaces to accept all presenters. Journals often act as archives for conferences they’re affiliated with, and will list those abstracts.

This means that none of Burzynski’s research from this journal has actually been peer-reviewed by the journal. The fact that he never actually published this data says a lot. Seriously – if you legitimately found something that helped cure cancer, prestigious journals would be tripping over themselves to have you publish in them. The fact that you can’t publish your research anywhere except in the occasional bottom-of-the-barrel shady journal means your research is terrible.

There was a final citation that stood out to me. It was the only citation that wasn’t research that Burzynski himself had done. Another key facet of science that makes it robust is that other scientists must be able to confirm your findings. And if they falsify your hypothesis, it’s back to the drawing board. So lets look at this one last citation:

11. Ogata, Y., Shirouzu, K., Matono, M., Ushìjima, M., Uchida, S., Tsuda, H. Randomized phase H study of hepatic arterial infusion with or without antíneoplastons as adjuvant therapy after hepatectomy for liver metastases from colorectal cancer. Ann Oncol 2010;21:víiî221 .

Again, this was a presentation made at a conference, specifically the 2010 European Society for Medical Oncology. Again, that means this research has not been peer-reviewed at all. In addition to the lack of non-Burzynski studies replicating his results, the National Cancer Institute also points out multiple studies (in legitimate journals) that are not able to replicate his results.

I would really like someone to take a look at the few papers Burzynski has published to see what the science looks like. One, I can’t access the couple of journal articles he actually does have because the journals are so crappy that my university doesn’t bother subscribing to them. But two, my area is population genetics and evolution, so I’m not really equipped to do an in-depth analysis of cancer research. But as a biologist I can safely remark on the quality of the journals his research was published in, and what that means.

So, Burzynski. Do you have any actual science to support your claims?

Update: I discuss further damning revelations about Burzynski’s research in this newer post.

A bully, plain and simple

Wow.

You know, I certainly understand the concept that not every stupid thing someone says is worth responding to. It’s the reason why I don’t devote a post to every time Ken Ham or Focus on the Family update their blogs. I also understand that sometimes people post terrible things with the sole intention of getting you riled up, and responding probably gives them some sort of smug satisfaction.

But sometimes, even the craziest of tirades deserved to be shared. Not because I think I’ll change the mind of the writer, but because people deserve to see what pure, unhinged, vitriol looks like.

This is a message to me from Abbie Smith of the blog ERV, with my response:

btw, my response to Jen:

Jen–
Rebecca Watson is a loser. She leeches off the skeptical movement to exist. Its disgusting.

You have (had?) potential to be more. And you are flushing it down the toilet.

You are in graduate school. That is your job. You spend way too much time going to these stupid conferences (hey, like Skepticon this weekend), that are not even tangentially related to your job (contrary to what you wrote in the small portion of your proposal I read).

Indeed, graduate school is my job. It is not, however, slavery. I thought you would understand that since you’re also a biology graduate student, but maybe they’re particularly rough over at the University of Oklahoma. You see, people – even graduate students – are allowed to have free time. Yes, we’re allowed to unshackle ourselves from the lab bench and head home for dinner. Some of us will read books or watch movies. Some will head out for beers with friends and coworkers. Some will even – gasp! – take vacations. We are allowed to have lives, and hobbies.

It’s intriguing that you claim I spend way too much time at these conferences, since you don’t know my schedule at all. Like how I purposefully did not schedule any speaking engagements for August, September, October, and early November because I knew I would have to spend extra time preparing for my Research Reports departmental presentation and the NSF fellowship proposal. Or how I’m not scheduling anything January through February because I’m preparing for my committee meeting and have to, as my 2nd year PhD student duties, run graduate student recruitment weekends. Or how I never schedule speaking events in back to back weeks, because I wouldn’t have the time. Or how if I have to miss a half day or day of work for travel, that I make up the time earlier that week or while traveling (which I can do since my project is currently completely computational).

But I’m sure all of the graduate students who decide to attend skeptical conferences will be glad to know that you have deemed them to be a waste of time.

And as for them not being “even tangentially related to my job”… Are you really saying that communicating science is not related to being a scientist? Would you say the same thing to students who spend their weekends helping with science fairs, or giving talks to classrooms or the community? I, like many scientists, want to be more than a pipetting machine.

These speaking engagements have given me much more practical experience in public speaking than most graduate students ever get, and it shows. I am consistently told by multiple professors in my department how excellent my speaking abilities are, and how clearly I can communicate my research.

You are behaving in an utterly unprofessional manner, posting pics of seminars you attend making fun of them, accusing your professors and classmates of being anti-science. The portion of your proposal I read was horrible, to the point of being shockingly horrible for someone of your education and writing experience. It bears absolutely no resemblance to my NIH proposal (which was funded).

This is a drastic distortion of what I’ve talked about here. Yes, I giggled at some particularly horrendous slides from a single seminar (not seminars) that the department as a whole was publicly cracking up about. And I have never accused my professors and classmates of being anti-science. I explained how because of the religious culture surrounding creationism, even some evolution-accepting scientists become uneasy about aggressively supporting evolution.

And while your comments about my proposal were probably meant to hurt my feelings and pad your ego (you got funding, good for you), it just makes me laugh. For one, the NIH fellowships don’t require a personal statement at all, unlike the NSF fellowships. And I explicitly stated my excerpt was from my personal statement, where you are required to talk about your motivation for becoming a scientist and doing outreach.

Second of all, it’s ludicrous that you think you can judge a 6 page application from two paragraphs of a personal statement. A draft personal statement that I openly admitted still needed revision, nonetheless. Unless you’ve been hacking into my computer and reading my finished application, I’ll just assume you’re bitterly taking pot shots. Especially since multiple professors and classmates have told me my application is excellent and very well written.

Which brings me to the worst part of your behavior, and why I know you are well on your way to becoming a professional loser– your proposal sucked, and you blamed your critique on your colleagues supposed anti-science. Youve already said your proposal isnt going to get funded ‘because youre an atheist’ or something stupid like that. And do I remember right, you didnt get into Harvard ‘because youre an atheist’ too, right? When you were properly chastised for behaving inappropriately and unprofessionally, you declared that it was because they couldnt handle you speaking out. Poor you for fighting the system! Career suicide! Bitch, please. I killed a Godfather of Retrovirology, and Ive still got a career (technically, it opened up locked doors for me). Heaven forbid your brain entertain the thought, for a moment, that you just fucked up. You are too stuck up your own ass to take responsibility for your own actions. Youre too old for this kind of immaturity.

My brain almost exploded from the irony that the same person who’s writing an unprovoked diatribe and coined the phrase “Rebecca Twatson” is the one calling me immature.

I’ve never said my proposal isn’t going to get funded because I’m an atheist, or that I didn’t get into Harvard because I’m an atheist. I don’t know why I ultimately didn’t get accepted to Harvard after my interview. And if I don’t get the NSF, it’s probably going to be because they don’t always like discovery based research without clear alternative hypotheses. My point in writing those posts is that I hate that I even have the inkling in the back of my brain that it may be because I’m an atheist. Because sadly, that shit happens. I know people who have lost their jobs because they were atheists, so I can’t help but worry and wonder. It’s one of the reasons I’m an activist – because I don’t think people should ever have to wonder that, even for a fleeting second.

But you can continue thinking I’m a sucky scientist with no social skills who can never admit she’s wrong. I don’t care, because I know it’s not true, and I know the people around me know it’s not true. I’ve demonstrated multiple times on my blog that I’ll edit, clarify, or even remove posts when I find conflicting evidence. I’ve greatly changed my talks because of feedback people have given me when they dispute certain points. And hell, in grad school I’m excited when I’m actually right. Classes challenge the way you think and what you think you know, and professors and classmates constantly challenge your data and interpretations. It’s how science works.

Oh, but right, I suck at that. Moving on.

If you went to my uni and you were in my department, you would be kicked out this coming Spring. And it would have had jack shit to do with your atheism.

But I am not your mother and you are not my problem. If you want to bitch on the internet for a living, more power to you. But you need to deal with the fact that people are going to call you a loser if that is what you choose to do with your life. Because you will be.

If you want to grow the fuck up and be a professional scientist, I would be happy to have you and happy for you.

But I just dont think its going to happen.

The irony of someone bitching on the internet about how I shouldn’t bitch on the internet.

It’s great to know that you would fire me just because you dislike a couple of things I’ve said about feminism (even though you apparently used to think I was awesome), and that you would make that decision knowing literally nothing about my academic achievements. How about the NIH training grant that I’m currently on? How about my two published papers? My grades? Work ethic? Scientific ability at all?

Nope, you know nothing, but you’d be childish enough to fire me.

You’re worried about my ability to become a professional scientist? I’m worried that you will become a professional scientist. We don’t need people who are so divorced from reality that they go on public, outrageous, denigrating rants. I’ll be the first to say that sometimes I can be a bit blunt, or rude, or abrasive. I don’t mince words when I have something to say. But what I’ve never been described as is pointlessly mean. Mean to the point where it’s frankly scary.

But really, it just makes me sad. I used to love your blog, but after “Elevator-gate” you did a Jekyll and Hyde. I can forgive people for occasionally saying something dumb or sexist or mean. But your cruelty isn’t occasional – it’s become an unhealthy obsession, with you lashing out like this at many different people. It’s not my place to psychoanalyze you on my blog, but I sincerely hope you find peace somehow. It’s one thing to strongly disagree with someone, it’s another to say stuff like this.