Friday, October 5, 2012

Patient Financial Policy - Update

Here's a copy of our new patient financial policy:

Without exception, we will not accept responsibility for any charges for materials or services unless the amount (or, at least, an upper limit for the amount) has been discussed with us, and agreed upon by us, prior to the materials or services being rendered.

By signing below, you indicate that you have read and understand our financial policy.

I described the story behind this, and the rationale, in this earlier blog post. Here's the first update on how it's going. So far, not promising.

The doctor/office that I complained about in that post was Dr. Elliot GoldStein, of Physician Associates, in Rockville, MD. After writing that post, I sent them a letter explaining my policy, and a check for the maximum amount that I thought I should be responsible for, $120. I also sent them a copy of the policy form, and asked that they sign and return it. Instead, I got a very terse letter in response -- he fired me! I've never been fired as a patient before, and it was very disappointing!

I wrote another response to them, just now, and all of these letters are copied in full below. Comments are very much solicited -- I'd really like to hear if anyone else has had similar experiences -- getting outrageous unexpected charges from doctors, and how you've dealt with them.

Here's the letter that I sent to him, in response to their bill:

September 16, 2012

Dear Dr. Goldstein:

I enjoyed meeting you and chatting with you, when I came in for a new patient visit this past August 16th. Unfortunately I think there has been a misunderstanding regarding the bill.

When I came to your office, before I went to the back to see you, I informed your staff of my financial policy, which is that I don't accept fees for any doctor's services unless I've been informed of the amount, and approved it, beforehand. I asked one of your staff the amount that I could expect for this visit, and they were reluctant to commit, but finally one woman did indicate that a routine office visit was $120. I again informed them of my policy, and that I wouldn't accept any charge higher than that, unless I was informed of it, and approved it, first. Unfortunately, I didn't get a record of this agreement in writing, because I trusted your office, and while I have been thinking of instituting this policy for a long time, I have not attempted to formalize it, until now.

So, I was shocked to receive the enclosed bill from your office for $342.23 (adjusted down from $400.26). After all, I met with you for less than ten minutes, and I remember, as I was leaving, that you said that I was an exceptionally easy patient, and that you wished all your patients were as easy as me. Furthermore, my wife also recently went to see you for the same thing, viz., a routine new-patient visit without any specific complaints, and she was only charged $198.73.

Because of this misunderstanding, I realize now that I must make this policy formal, and so I'm enclosing a form that I would like you or someone in your staff to sign and then return to me.

I'm also enclosing $120, which is the amount that I believe I should be responsible for, for this visit. I realize that I made a mistake in not formalizing my policy prior to my visit with you, so I'm willing to be a little bit flexible regarding this amount, but under no circumstances will I accept $342.23. I'm CC'ing this letter to my insurance company, so that they can adjust the amount they apply to my deductible.

If you would like to read more about this patient financial policy, and the motivation behind it, I invite you to read my blog post at this web address:

I hope this experience doesn't sour our relationship -- I did enjoy meeting you and am hopeful that my wife and I can be your patients for a long time into the future. However, I insist that I be informed of what my financial liability will be, in each case, before I can be assumed to be responsible for it. To me, it seems to be an eminently reasonable and fair requirement.

Yours truly,

Chris Maloney

In response, I received the following very terse letter, terminating our doctor-patient relationship!

October 4, 2012

Mr. Christopher F Maloney,

This practice finds that it is unable to provide care that is satisfactory to you. We recognize that some physician's offices and patients cannot come to a satisfactory doctor-patient relationship without fault being ascribed to either party.

Please refer to the directory of physicians provided by your insurance to select another physician and practice in your health plan.


Physician Associates

And finally, the letter that I just wrote back to them:

Dear Dr. Goldstein:

The letter we received from you today was very disappointing. After all, I went to your office in good faith, and trusted your staff and yourself to treat me with respect and integrity. In response to the misunderstanding about the fee that you charged, I took the time to write a detailed, courteous letter to you. Your response was very terse (basically just a form letter) terminating our doctor/patient relationship. I think that I deserve more consideration than that.

I would like to ask you which of the points of my letter, in particular, you object to. Was it that I took issue with the amount of the bill that you sent, $342.23? Or was it my request that you sign our "Patient Financial Policy"?

If the former, then I wonder whether you doubt my story, that I explained my policy to your staff, and was quoted a price of $120? I'd also like to understand how it is possible to justify a charge of $400.26 (the original amount billed to the insurance company) for a visit that took less than ten minutes.

If the latter, then I would really like to know your opinion about a patient's right to know the amount of financial responsibility he or she incurs, before a service is rendered. Don't you think this is a reasonable request? Perhaps you remember that when I saw you, I mentioned that both of my parents are retired physicians. As a "sanity check", I asked them what they thought of this policy, and they were both in favor of it, and thought it was reasonable and appropriate. It seems to me that the health-care system has moved so far away from the idea of "fee for service", that now the patient is completely cut out of the loop. Don't you see that as a problem?

Because I feel strongly that this is a systemic problem in our health-care system, I have posted my letters and your response on my blog, here: .... I would be very happy if you would respond to me with answers to some of these questions, either in another letter, or, if you prefer, in a comment on my blog.

Thank you for your time,

Chris Maloney

Wednesday, September 12, 2012

Patient Financial Policy

I just happened again. I went to a doctor's office, saw the doctor for less than ten minutes, and then later, was slapped with a bill for over $300. This is the second time in a few months that this has happened, and I'm not going to put up with it any more.

Being of reasonably good health, I don't visit doctors very often. Until recently, I haven't had a regular general-practice doctor. There are several reasons for this; not in any particular order, they are: moving around a bit, not enjoying going to the doctor's office, not having a good reason to go, and not being particularly impressed with the doctors that I have seen. Because I don't have a regular doctor, it seems that when I *do* go, I am almost always a new patient, and have to fill out reams of forms related to my medical history, and various waivers and agreements. Lately, these packets always include a "doctor's office financial policy", which always contains, among various obnoxious provisions, a statement that I agree that I'll be responsible for whatever the office decides to charge for any and all services that they provide.

These days, every time I've gone to the doctor, when I'm walking out of the office, I have no idea what the financial liability is that I've just incurred, and usually don't even have a good idea of what services were just provided. The services (much less the charges) are never explained; they always just say, "you're done". They expect me to trust that: A, the services rendered were worthwhile and justified; and B, that the amount charged was fair and reasonable. The problem is, I don't trust them anymore.

Therefore, we've just established a Patient Financial Policy. As a family, we've decided that from now on, whenever one of us visits a doctor or goes to a hospital, we'll require them to sign this before any services are rendered. It states, very simply, that we won't accept any charges that we haven't been made aware of first. It's very simple: we just want to be informed of the fees beforehand. There's no implication that we won't accept the fees, or even turn down the services (although, of course, that's our right -- isn't it?) but rather, just that we want to know what the charges will be, before we agree to them.

On the face of it, this seems like such a no-brainer, that it's incredible that we'd have to ask for this agreement. After all, it's our money -- and it's our perogative to know what we'll be getting when we spend it, and how much it's going to cost. I don't think that it *should* be a problem for any doctor's office to agree to this, but I expect that it *will* be, for a number of reasons.

The first has to do with a general attitude of the staff at most offices that I've encountered, that these fees are for the doctor's office and the insurance companies to decide, and are really none of the patient's business. When, in the past, I've tried to push for some accountability or information, the response has been, "don't worry about it, it's covered by your insurance." This is galling for two reasons. This year and last, we've switched to a high-deductible insurance policy, which means that, unless we have abnormally high medical bills, we probably won't meet our deductible, and thus, we'll end up paying all of these charges ourselves. The other (and this is the stronger reason, I think) is that this attitude is just plain *wrong*. It assumes that because I won't be personally responsible for the bill, that I shouldn't care what the amount is. This is akin to marking up library books, or abusing a rental car, I think. Why should I care how much damage gets done, if I'm not going to have to pay for it myself? But these covered costs are borne by all the insured patients, collectively, and each one of us should feel responsible for keeping our own charges as low as possible, so as not to be an extra burden to everyone else.

The next obstacle I've encountered is that these offices, and the health-care system in general, these days, doesn't seem set up to be able to provide this information. When I was at the office visit that I mentioned at the top of this post, I asked how much the visit would cost, and they actually told me that they had no idea -- that it depended on too many variables, and there was no way they could provide me with a number. I asked what was the charge for a normal office visit, and they couldn't even give me that, because they said it depended on what type of insurance I have. I have to ask, what kind of sense does this make? When and how, exactly, did we all slip into complacency about this ridiculously unfair system, whereby each insurance company negotiates separately with each doctor's office for the fees for particular services? Doesn't this mean that someone without any insurance will always get the highest charge, because they don't have anyone to negotiate for them?

Well, I know that this particualr issue is too big of a fish for me to fry. So that's why, in the policy, instead of insisting that I be informed of the exact charges, that I've added the weasel-words, "or, at least, an upper limit for the amount". Any doctor's office should be able to tell us how much they would charge that unfortunate, uninsured wretch who stumbles into their office, with nobody to negotiate prices for him, shouldn't they?

Finally, one last thing that I need to whinge about is the patronizing attitude that I've often received, that I would have the temerity to question that some service or procedure is not worth the fees being charged. They seem to be asking, "Don't I know that the doctor is always right?" Or to be implying that when it comes to health, there should never be any consideration of the cost. But, in fact, *everything* should be subjected to a cost-benefit analysis. Everything. Yes, I know there are risks for postponing or avoiding certain tests -- but there are risks associated with everything in life, like driving a car, or going skiing. Ultimately, it's my perogative to decide (in the case of my own health, at least) when the costs outweigh the risks.

In addition to the policy itself, I've compiled an office visit checklist that I will print out and bring to every doctor's visit from now on. Comments are welcome, either here, or on either of those Google docs!

I'm going to be putting this into practice starting tonight, and I'll post back here occasionally to report on how it goes -- whether the offices accept the policy, or not. I'm actually hopeful that this idea will catch on with others, because I think if we can start a movement, then maybe some of these attitudes will change.

Sunday, July 22, 2012

On replicability and standards for bioinformatics software

In this post I'd like to introduce an issue that I've been reading about lately, reproducibility of bioinformatics results, and the quality and availability of software that is written by researchers. C. Titus Brown, who writes the blog "Living in an Ivory Basement", wrote an excellent post on this topic recently, "Our approach to replication in computational science". It is well worth a read.

The take-home message is that most software and data that gets published nowadays (usually in the form of supplementary material to a journal article) is of poor quality, not reusable, and generally not conducive to reproducing the results of the research. This is a shame because, especially in the field of bioinformatics, new techniques and algorithms often build upon earlier work, and if that earlier work were easily available and reusable, then it would be of much greater benefit to the advancement of the field.

This post is also good because the author writes details about the tools and processes that he has used, and it could serve as an excellent tutorial and jumping-off point for anyone interested in learning how to produce software in this way.

In the last few days, I've run across a few other resources on this same topic:

  • Slides from a BOSC Panel discussion slides, by the same C. Titus Brown. This is short and readable, and suggests:

    • There should be standards for the review of software, just like there are for the review of article texts, as part of each journal's review process;
    • The focus of that review should be on replication of the results;
    • A web site should be set up to facilitate software reviewers, with checklists and dynamic features to facilitate scoring.

  • A blog post, "Scientific papers and softwares", on, about this same topic, by "leprevost".

  • A response to that, 'Response to "Scientific papers and softwares"', also on, by Joel Berger. Joel is very active in using Perl for science, and he recommends using Github for version control and project management, and uploading all the Perl software that you develop to CPAN (the Comprehensive Perl Archive Network).

Finally, for those interested in getting involved in the community of scientist who are using Perl (or Perl programmers who are doing science, if you prefer) there is the Perl4Science site that Joel Berger created, and the The Quantified Onion Google group (basically, a mailing list).



  1. C. Titus Brown on Twitter
  2. C. Titus Brown's blog, Living in an Ivory Basement.
  3. "Our approach to replication in computational science", blog post by C. Titus Brown, 4/2/2012
  4. BOSC Panel discussion slides, by C. Titus Brown, on Slideshare
  5. Bioinformatics Open Source Conference 2012 - conference web site
  6. "Scientific papers and softwares", blog post on, by leprevost, 7/12/2012.
  7. 'Response to "Scientific papers and softwares"', blog post, also on, by Joel Berger, 7/12/2012.

Sunday, July 8, 2012

The JATS-To-Mediawiki Project

Lately I've been spending a bit of time working on a project that was started by Daniel Mietchen, to develop a tool that will convert JATS documents (like the open-access biomedical journal articles on PubMed Central) into Mediawiki format, so that they can be uploaded onto a wiki. This is just one sub-task of his Encyclopedia of Original Research (EOR) project.

The essence of the EOR is distilled, I think, by a quote from John Wibanks from a post in 2009 , "Science is already a wiki if you look at it a certain way. It’s just a really, really inefficient one". He was referring to the way that science progresses through a massive collaborative effort, where researchers amend, revise, and extend the work of those who came before them. So the EOR, which is based on Mediawiki (the same wiki software that runs Wikipedia) is designed to make it much more efficient. Note that Wikipedia itself would be inappropriate for this system, because of their "No original research" policy.

You can read more about the rationale and scope of the EOR and JATS-To-Mediawiki in a paper proposal that we wrote for JATSCon 2012.

The JATS-To-Mediawiki project is hosted on Github, and is still in a pre-alpha stage. Jeremy Morse and Konrad Foersner are collaborators, and Jeremy has done almost all of the work on the XSLT stylesheet, which is the heart of the project.

Here are some step-by-step instructions for trying it out. It's assumed you have access to a Unix box, and a Mediawiki installation somewhere that you can use for testing. If you want to use my test wiki installation at, go ahead.

First, download and extract the Github project files, and set an environment variable to point to that directory

  wget --no-check-certificate \
  unzip master   # this creates konrad-JATS-to-Mediawiki-...
  export JTM=`pwd`/konrad-JATS-to-Mediawiki-...

Download the sample files, using the script


This creates a directory called "samples", and downloads seven articles from the PMC Open Access Subset. The XML files are the only ones that we are interested in (so far). They all have an ".nxml" extension, and you can find them easily:

  $ find -name '*.nxml'

Pick any one you want, or download your own sample, and convert it with something like:

  cd samples
  xsltproc --novalid $JTM/jats-to-mediawiki.xsl PMC1762412/pone.0000133.nxml \

Next, in your browser, go to the import page of your test wiki; for example, Click "Choose file", and select the file you just created, and then click "Upload file". That should return with a link to the new wiki page; in this case, The Sound Generated by Mid-Ocean Ridge Black Smoker Hydrothermal Vents.

As I mentioned, the project is still at an early stage, and there are still many things to do.

Friday, May 4, 2012

Fixing Wikipedia links to GeneReviews

Yesterday I was finishing up the final bit of homework for a course I'm taking, and came across a problem with a Wikipedia page. I think I fixed it, but it was not particularly easy, and I'd like to write about it here.

The problem was with one of the Wikipedia infobox templates, and the way that it generates links to the NCBI GeneReviews site.

The immediate problem that I discovered was on the page Hyperkalemic periodic paralysis. On that page, there is an infobox on the right that has a link to GeneReviews, but the link is broken. It goes to

This URL unfortunately mixes an old-style NCBI bookshelf URL with a new-format ID number. The correct URL is any of the following.

This Wikipedia page uses a template to generate this box -- one of many infobox templates. This infobox in particular uses the Template:Infobox_disease. From the documentation, you can see that this template provides fields that editors of Wikipedia pages can easily fill in. When the page is rendered, the template code gets executed to generate the nice tabular display, with links, from the values in those fields.

This particular infobox has an accompanying documentation page, test cases page, and a sandbox. The template itself is protected (can't be edited by the average user) because it is used on hundreds or thousands of pages. So, the sandbox provides a place where someone (me) can try out changes, before submitting an "edit request" to one of the admins.

The infobox template code is pretty intimidating-looking, but I stared at it for long enough, that it eventually started to make sense to me.

The immediate problem stems from the fact that there are two types of IDs to refer to these GeneReviews resources: one "human readable" (e.g. "hyper-pp") and the other alphanumeric ("NBK1496"). The problem that I discovered was due to the fact that someone entered the alphanumeric ID, when she should have entered the human readable one. In other words, the template fields were given like this:

GeneReviewsID = NBK1496 |
GeneReviewsName = Hyperkalemic Periodic Paralysis Type 1 |

but they should have been given like this:

GeneReviewsID = hyper-pp |
GeneReviewsName = Hyperkalemic Periodic Paralysis Type 1 |

I'm sure that there are lots of places where this template is used correctly, with the human-readable ID, and it wouldn't be possible for me to find all of them and change the human-readable ID values to alphanumeric. So it's important that the human-readable ID values continue to work.

On the other hand, when we redesigned the NCBI bookshelf, we made it very hard for anyone to find this human-readable ID, and so it is understandable that the editor of this page used the NBK number. The NBK number is really the only visible ID. So it's important that these new ID numbers should be able to be used.

Therefore, the only way to fix this problem that I could think of was to define a new field, which I called GeneReviewsNBK, and to "deprecate" the old one. The old one should continue to be supported, and should generate correct URLs, but people should be encouraged to use the new NBK number going forward.

The logic to generate the new links for this infobox item turned out to be a bit complicated. It does different things depending on whether the old-style GeneReviewsID was given or the new-style GeneReviewsNBK, and the link text also depends on whether or not the label GeneReviewsName was given. Here it is:

| label10     = [[GeneReviews]]
| data10      =
  {{#if: {{{GeneReviewsNBK|}}}
    | {{#if: {{{GeneReviewsName|}}}
        | [{{{GeneReviewsNBK}}}/ 
{{{GeneReviewsName}}}] | [{{{GeneReviewsNBK}}}/
{{{GeneReviewsNBK}}}] }} | {{#if: {{{GeneReviewsID|}}} | {{#if: {{{GeneReviewsName|}}} | [{{{GeneReviewsID}}}/ {{{GeneReviewsName}}}] | [{{{GeneReviewsID}}}/ {{{GeneReviewsID}}}] }} }} }}

The syntax for this is described in the MediaWiki Help:Extension:ParserFunctions page.

I edited the sandbox with this, and created a test page in my user area to try it out, and finally was able to get it to work. Then I:

Assuming my edit request gets implemented, then, I'll go back and fix the original problem page with the new NBK number.

Friday, January 13, 2012

Open Letter to Johns Hopkins University Press, should publicly oppose the Research Works Act

Dear Ms. Keane:

I'm writing this open letter as a student of Johns Hopkins University, to urge the Johns Hopkins University Press to publicly oppose the Research Works Act (HR 3699), and to terminate your membership in the Association of American Publishers (AAP).

Other writers on the Internet make the case for this better than I could, so I'd like to refer you to a few online resources.

Recently, various other organizations have publically disavowed the RWA, and/or resigned their membership in the AAP, including

I would like to suggest that this is an opportunity for Johns Hopkins University Press to lead, by coming out quickly and forcefully in favor of open access to scientific literature, which is so crucial to accelerating the advancement of science. I note that you've recently started a JHU Press Blog and I think that would be an ideal venue for this type of report.

Thank you for your consideration!


Here are a few other blog posts I've seen recently urging this kind of action:

Monday, September 19, 2011

Letter regarding open access self-archiving at Johns Hopkins

The following is a letter that I just sent to some faculty and staff at Johns Hopkins University, regarding their policies about open access, their instititutional repository, and whether or not they have a mandate in place requiring their researchers to self-archive their work.

I debated with myself for some time about whether or not to put this letter on my blog. I finally decided in favor of openness. I think that this might serve as a test case for others who might be interested in this issue, and who might be considering advocating for such a policy at their own universities. I will post follow-ups with the results of this experiment. Feedback is very welcome.


This email is to inquire about Johns Hopkins' policy with regards to open access self-archiving of author’s refereed journal articles. I am a student at Johns Hopkins (recently started as a Master's degree candidate in Bioinformatics) and a software developer by trade. I also have a strong interest in open access tools, policies, and methods. So, I am writing this email to introduce myself, and to ask some questions about Johns Hopkins' policies regarding some of these issues, and perhaps to stimulate some dialog.

I have recently found and read your "Johns Hopkins Scholarly Communications Group" site, and see that it says that you are "dedicated to fostering open access". I found (most of) your names from this site, and looked up your email addresses in the JHU system.

I see that JScholarship is the primary institutional repository for JHU -- is that right? Are there others? According to ROAR it uses the DSpace software. I browsed the site for a while, but didn't find very many journal articles. Would it be fair to say that currently, not a high percentage of the research papers produced as output by JHU researches is "self-archived" on JScholarship? If that's true, is there some other repository that they do use, that I haven't found yet?

The Scholarly Communications Group site also links to the Johns Hopkins Electronic Publishing Project. From there, I found the Mark Cyzyk's and Sayeed Choudhury's excellent paper from 2008, "A Survey and Evaluation of Open-Source Electronic Publishing Systems" (Wiki home; PDF whitepaper; on JScholarship; PowerPoint slides). It looks like the system that was most favored by that paper, "Open Journal System", was installed to this Electronic Publishing Project. But, it seems that, perhaps, it is no longer being actively maintained. Is that right?

I've recently been reading a lot of the writings of Stevan Harnad, who is a strong advocate of institutional repositories, and of policies that mandate self-archiving by authors, in order to further open access to scientific research. Below are a couple of links to resources related to this, that may be of interest. (Note that there is some redundancy in the material covered by these various links.)

Does Johns Hopkins have a mandate planned or in place requiring its researchers to self-archive the products of their JHU-funded research, along the lines of the other 130 institutional, 33 sub-institutional, and 52 funder mandates currently indexed in ROARMAP (including Harvard, MIT, Duke, Oberlin, Emory and NIH)? Has this been discussed at JHU? If not, what might be some good avenues that I and other interested students and faculty could pursue to help promote this goal?

Thank you very much for your time! Here are the links/resources:

Again, thank you very much for reading this email, and I’ll anxiously await your reply.

Chris Maloney