OMF progress

[Murph]

I have never heard such a thing before, where did you read this? I know that with the open access journals, which sometimes do not require peer review before publishing, people worry that this may allow poor quality science to be published. But that's not an issue with traditional journals, which require that a paper passes peer review first before publishing. I've heard nothing about such journals being "rotten at every layer".

Hi Hip

I agree that 'rotten at every layer' is a strong claim! I'll not claim that the system is irrevocably broken. after all, it's got us this far.

The issues with the journal system (as it is practised rather than as it might be in a better world) include pressure to publish, consensus around the importance of p values, p hacking, the file drawer effect, positive result bias, the profits journal makers have, predatory journals, the relative impact of 'top' journals and the effect of publishing in them on careers, journals publishing in a way that prioritises their impact rating rather than good science, pressure for citations, lack of replications, etc.

I've learned about most of these by following Andrew Gelman and the crisis of replication (which goes far beyond just psychology.) You can get a quite nice overview here.

Many of these issues are not isolated in the journals but exist where that system rubs up against other institutions. I think it's important to see what Ron's doing (and the existence of PlosOne, etc) as part of a protest against this system in an attempt to improve it. It'd be fair to say there has been some progress already.

Ron's experience in avoiding journals comes from the Human Genome Project where they just put the results online. You can see Ron arguing quite persuasively against the existing system in this video (from 4 minute mark onward)

 

[Hip]

In any particular area of study, everybody knows everybody else, making genuinely unbiased peer review impossible.

Knowing other people in your field does not necessarily mean they like you or support your ideas. You are just as likely to get your paper reviewed by experts who are somewhat skeptical of your ideas.

Being seriously vaccine damaged myself, I am highly sceptical of all the peer-reviewed papers showing vaccines to be absolutely safe, and sick and tired of the scapegoating of Andrew Wakefield for having the nerve to do a preliminary study which gave the wrong answer, and for charging the participants costs.

Andrew Wakefield is the man who now gives talks on conspiracy theory ocean cruises. I can't think of a more obvious sign that someone is dealing is suspect science. I am not denying that vaccines might trigger diseases like ME/CFS, but you can't do conspiracy theory cruises and expect to be taken seriously as a scientist.

 

[Mel9]

Hi Hip

I agree that 'rotten at every layer' is a strong claim! I'll not claim that the system is irrevocably broken. after all, it's got us this far.

The issues with the journal system (as it is practised rather than as it might be in a better world) include pressure to publish, consensus around the importance of p values, p hacking, the file drawer effect, positive result bias, the profits journal makers have, predatory journals, the relative impact of 'top' journals and the effect of publishing in them on careers, journals publishing in a way that prioritises their impact rating rather than good science, pressure for citations, lack of replications, etc.

I've learned about most of these by following Andrew Gelman and the crisis of replication (which goes far beyond just psychology.) You can get a quite nice overview here.

Many of these issues are not isolated in the journals but exist where that system rubs up against other institutions. I think it's important to see what Ron's doing (and the existence of PlosOne, etc) as part of a protest against this system in an attempt to improve it. It'd be fair to say there has been some progress already.

Ron's experience in avoiding journals comes from the Open Genome Project where they just put the results online. You can see Ron arguing quite persuasively against the existing system in this video (from 4 minute mark onward)

What a wonderful talk by Ron Davis! I myself have often reviewed papers. In some instances I have the opinion that the paper is fine, with minor changes required. Yet, the other reviewer has completely failed the paper or insist the authors need to do more experiments. I strongly suspect that many scientists who are requested to review research papers feel insecure in the science and that causes them to feel they need to be overly critical. Ron's suggestion that they may be in their first year of post graduate work probably fits that theory.

However, in most cases, in journals run by scientific societies, reviewers chosen are known researchers in the field and tend to be fair and much more accomodating (we don't all aim for Nature).

 

[Hajnalka]

I'm not well enough to read every post, so apologies if it was already mentioned. But while Ron Davis heavily criticises the current reviewing system and doesn't play by the rules and makes results available - he never said that they're not going to publish (just that it's not their top priority). He said e.g. that the reason they couldn't publish about the nano needle so far is that they don't fully understand why it is working yet.

 

[Ben H]

Is it just me and my desperation/impatience but is anyone feeling that progress from OMF is a bit slow. I know they are doing their best but I wonder if all the metabolomics and analysis of metabolites in each patient is actually going anywhere. It sounds like it could be going towards personalised medicine which is too big a leap right now. I would prefer to hear how many fda approved drugs they have tested and how that is going. I'm starting to feel reluctant to keep pouring my money into them. Maybe that is lousy to say and I am not seeing wood from the trees.

Hi @neweimear

I have only just got round to seeing this.

@Jesse2233 has made some good points already as have many others in addressing research in general, but Prof Davis and his team are working as fast as possible. That is one reason they have not published their findings yet-so that they can focus purely on the science and pushing that forward as fast as possible (publishing takes a lot of time). However they are working on publishing now and adding to the collective. Analysing the data from the Severely ill study also takes a lot of time simply because of the huge amount of data generated-NOTHING like this has ever been undertaken before. Again the same can be said about working with such a vast array of scienctists with the 'open data' approach.

I really hear the desperation-I am bedbound myself and have been ill for 5+ years. It is so difficult waiting but it is comforting knowing they are working around the clock. MECFS is a very complex problem, and that will inevitably take some time.

Hopefully we can get an update soon.

Thank you so much for your donations. They are helping fund the research we so desperately need.

Hang in there, and if you can please tag me @Ben Howell anytime if I need to be contacted to pass something on


Ben

 

[Deepwater]

Knowing other people in your field does not necessarily mean they like you or support your ideas. You are just as likely to get your paper reviewed by experts who are somewhat skeptical of your ideas.





Andrew Wakefield is the man who now gives talks on conspiracy theory ocean cruises. I can't think of a more obvious sign that someone is dealing is suspect science. I am not denying that vaccines might trigger diseases like ME/CFS, but you can't do conspiracy theory cruises and expect to be taken seriously as a scientist.

I didn't say he should be taken seriously as a scientist - I'm not a scientist so can't comment on his science. But this is an ad hominem argument and doesn't address the science anyway. What I was trying to say is that I find it tiresome that this one little paper by a lone individual is so successfully trawled around by the hugely well-funded and powerful vaccine industry as a distraction technique/ straw man with which to beat down any opposition (mixed metaphors entirely my own responsibility). I have absolutely no doubt that, had his conclusion been that the MMR is safe, his paper, with all the same flaws, would have stood. I know this is somewhat off topic, but if you really think it possible that vaccines may sometimes cause ME, and if you have experienced ME in any severity and know what that feels like, then does that not really concern you?
Less off topic is the point that the journal system is skewed by many factors, as @Murph has indicated, but medical science in a more general sense is perhaps most heavily skewed by the huge amounts of money to be made (on sales), or lost (on compensation payments) if treatments turn out to have caused harm.

 

[Ben H]

I'm sure they're working their butts off, but just not talking about it. I want more communications from OMF.

If you put Open in the name of the organisation, run on donations, and promise not to publish in official journals, it's fair that expectations for communication are an order of magnitude higher than for other researchers. They have a monthly newsletter but it's far from a candid look at what's going on researchwise. More of a call for donations. SMCI is good with scientific comms and they could replicate that.

Ron doesn't have to be the only spokesperson and I don't even necessarily need to hear results (I know they plan to share data with other researchers thru their research portal). I'd just like to hear what's underway and gets regular updates on timelines. What little things are going on? Who's hired and fired; who's meeting who; how many peopel came in for a blood draw; what sort of test tubes got delivered from Thermo Fisher and why; did Bob Naviaux email thru an interesting paper he saw; Does Wenzhong Xiao now have to rent an extra ten terabytes of data storage; which staff member is having a birthday? All these little things help make us feel like we see inside the organisation we're funding.

Perhaps give someone who works there permission to run an Instagram account where they take shots and chat to staff on what theyr'e up to...

Hi @Murph

There are some good suggestions here. I will pass them on.

We have just started 'Science Wednesdays' which will hopefully give more of what you are asking for:

https://www.omf.ngo/science-wednesday/

I would like to say however that we have recently (August) had the live Community Symposium which talked about the science in a lot more detail and was livestreamed free across the world. Again this is unheard of in the MECFS community. We also had a Q and A and update with Prof. Davis not long before that. But I do understand and get your point, your comment about Wenzhong made me laugh out loud!

I take your point about the 'Open' in the name and expectations and can understand, though it also is referring to the open platform OMF have for sharing data with researchers. There is a link on the OMF website where any researcher, providing valid credentials etc, can view the data that has been generated so far. I believe its a work in progress and am not sure how far they are with it yet (as I am not a researcher) but again this is unheard of. OMF and Prof. Davis really are pushing the boundaries in the interests of finding the answer as fast as possible (and change the status quo as you have referred to in your post).

I will pass on all that you have said in your post.

Thanks,


B

 

[Hip]

But this is an ad hominem argument and doesn't address the science anyway.

That's not an ad hominem argument. For a scientist to hang around with the conspiracy theorist crowd and to make his income from these people is analogous to a vicar hanging around in brothels and financially benefiting from prostitution.

Andrew Wakefield's scientific reputation was in tatters in the UK, after it was shown that his MMR study was suspect and manipulated, and after it was uncovered by journalists that he had a whole business model set up to make money out of the anti-vax crowd. So Wakefield left the UK, and set himself up in the US, where he pandered to the huge anti-vax and conspiracy theorist audience in the States, an audience which includes Donald Trump, who likes Wakefield's theories. Wakefield is pretty good at following the money. I would not feel sorry for him; he's doing very well for himself.

I know this is somewhat off topic, but if you really think it possible that vaccines may sometimes cause ME, and if you have experienced ME in any severity and know what that feels like, then does that not really concern you?

Of course I would like to see safer vaccines, and a better understanding of why vaccines may sometimes trigger disease; but my general stance is that lack of vaccines is the major cause of ME/CFS. If we all had childhood immunizations against coxsackievirus B, echovirus, Epstein-Barr virus, HHV-6 and cytomegalovirus, I think ME/CFS would be pretty much banished as a disease, except for rare cases here and there.

The area where I think it's possible that vaccines may have dramatically increased the prevalence of ME/CFS is the poliovirus vaccination program. See this thread: Did the introduction of the polio vaccine cause the massive rise in ME/CFS incidence in the 1980s? But if true, that only underlines the dire need to introduce a coxsackievirus B vaccine.

I don't share your pessimistic views that papers on vaccine adverse effects are suppressed. In the case of the GlaxoSmithKline H1N1 pandemic flu vaccine that triggered cases of the autoimmune disease narcolepsy, this fact was acknowledged by GSK, and the study examining the mechanism by which this vaccine may have triggered narcolepsy has been published without any problems.

 

[Nickster]

Dr Ron Davis has the most unique approach to solving this huge medical issue. I would call him the Einstein of our generation because he is breaking rules and doing what will get him the best results for testing, collaborating with other medical professionals and communicating his findings with all of us (the sick and their caretakers). This is a rarity! His driving force is not money nor power nor fame. He truly wants to solve this and he has the brains, tenacity and compassion to do it.

Ron, Janet, Whitney and Ashley have brought this disease to the surface and people now understand this disease is very real. It now has attention and the medical field has to address it.

I think he just may solve it.

Thank you to our rogue doctor!

 

[AshleyHalcyoneH]

I'm sure they're working their butts off, but just not talking about it. I want more communications from OMF.

If you put Open in the name of the organisation, run on donations, and promise not to publish in official journals, it's fair that expectations for communication are an order of magnitude higher than for other researchers. They have a monthly newsletter but it's far from a candid look at what's going on researchwise. More of a call for donations. SMCI is good with scientific comms and they could replicate that.

Ron doesn't have to be the only spokesperson and I don't even necessarily need to hear results (I know they plan to share data with other researchers thru their research portal). I'd just like to hear what's underway and gets regular updates on timelines. What little things are going on? Who's hired and fired; who's meeting who; how many peopel came in for a blood draw; what sort of test tubes got delivered from Thermo Fisher and why; did Bob Naviaux email thru an interesting paper he saw; Does Wenzhong Xiao now have to rent an extra ten terabytes of data storage; which staff member is having a birthday? All these little things help make us feel like we see inside the organisation we're funding.

Perhaps give someone who works there permission to run an Instagram account where they take shots and chat to staff on what theyr'e up to...

Thanks for this advice! I think an Instagram is a great idea. Part of why there aren't more detailed updates frequently is because the lack of funding makes us constantly understaffed for things like communication, etc. It's sort of a one man show for all of that. So we are doing our best. We hope to come out with another video of Ron maybe this December to say what's been happening. But if people would like small progress updates like you suggested, or even just "hey, we're celebrating a birthday!" an Instagram account is a great idea! We really appreciate the input, thank you!

 

[Murph]

Thanks to @AshleyHalcyoneH and @Ben Howell for responding positively to my suggestion. I'm excited about Science Wednesdays!

I acknowledge that comms is hard. That's why communications is a profession all of its own!

One rule of thumb is to acknowledge that each piece of comms won't hit all your stakeholders. A certain level of redundancy is considered a good idea. If you want to create the impression of monthly comms, you need to go more than monthly, etc.

Obviously there's the PR crowd who go digging for every post by ben and janet, but the median stakeholder doesn't see each thing. A practical application of this advice: you could repurpose little snippets from Science Wednesday in other places and link back to it.

It's also obviously a short-term trade-off. Paying someone to do comms work creates an opportunity cost. That said, good comms overcomes the opportunity cost over a longer time horizon. The potential usefulness of good comms can be seen in that Stanford Magazine piece the Problem Solver, and, more than anything, in Unrest.

 

[bspg]

OMF already has an Instagram page, unless this ones a fake...

https://www.instagram.com/openmedf/

 

[Janet Dafoe]

Hi,
I just read this entire thread to Ron. Between the writing of two grants (very time consuming), and holding a big symposium, he has been super busy, and the research has been ongoing during this, albeit at a slower pace. Now the group is back to full steam ahead research. They are working on all their different projects, working hard on getting out some publications, and Ron, Ashley, Raeka and I are working on ways to communicate more frequently.
Ron spoke informally for about 3 hours at our local Bay Area Support Group meeting, and a video was made of that. We want to make it public, but it's a huge file and the group leader and Ashley have to figure out how to deal with it.

Ron says they are making good progress on lots of research fronts. Sometimes there are tiny little breakthroughs, like figuring out how to clean our nano needle chips so they can be re-used instead of having to make new ones (very time consuming nano fabrication). Rahim finally figured out how to do this and it's going to really help make the research go faster. They are also figuring out how to store the blood so that it continues to give us accurate results after storage. Up till now, each sample had to be processed within 20 minutes and the nano needle procedure had to be done right after the blood was processed. Rahim has had to work till 3-4 am on these experiments, especially if he gets the blood at 4 pm. When they figure out how to store it so it can be used for a longer period of time, things will go faster.

Ron usually waits till he has somewhat of a story to tell you before he makes a video. Maybe you'd like smaller chunks. One of the problems with this is that good science often gets things wrong and then they go back and regroup. Ron worries about putting out things that are wrong. But if he puts out things as the work progresses, people will need to realize that things could change as the research progresses. He likes to put out ideas that MIGHT be true, and are interesting to think about, but might NOT be true. Pay attention to his qualifying words, like MIGHT, and COULD BE, POSSIBLY, PROBABLY, MAYBE, etc.

Ron says, "Discovering barriers to making rapid progress on the research can be frustrating. For example, we have just learned that how some of the biobanks have archived their samples makes it such that they won't work for our studies. They were stored incorrectly or processed too slowly. Many things really matter: the type of tubes, the speed of processing after the draw, the temperature it's stored at, how fast it's frozen, etc. All these kinds of problems make the research slower and it's very frustrating. We continue to work on this and are trying to communicate with other researchers how to best store samples". and "Eventually I will communicate about the publishing issue because there are some misunderstandings here".

Do you guys like hearing about little stuff like this? Ron would like your feedback!

Thanks for all your thoughtful posts.

Janet

 

[Murph]

Do you guys like hearing about little stuff like this? Ron would like your feedback!

Janet

Thanks heaps Janet! Hearing about the setbacks in using various biobanks and imagining tiny nanoneedles full of gunk is illuminating and useful and helps us feel like we're down there in the trenches.

I definitely don't want to wait to only hear the answers and I don't think other people want to either: An engaging story has the struggle along the way not just the triumph at the end (otherwise books would be a lot shorter!)

Thanks again for sharing with us.

 

[bspg]

Do you guys like hearing about little stuff like this? Ron would like your feedback!

Thanks for all your thoughtful posts.

Janet

Thank you for the update @Janet Dafoe (Rose49). I personally love hearing smaller updates but I do worry about people missing the "qualifiers". Between the excitement over an update and pervasive brain fog, qualifiers could be easily missed.

On the other hand, PR members are AMAZING when it comes to discussing research and it's likely that any misunderstandings would be corrected quickly.

I really liked the YouTube videos of Ron in the lab explaining what he's been working on, but I realize that's probably not a convenient way to do smaller updates.

 

[Janet Dafoe]

(otherwise books would be a lot shorter!)

.

Ron really laughed at that. He said, " Yeah, my books are only 2-3 pages!" He doesn't often laugh out loud in a belly laugh. You did it!

 

[Learner1]

. He likes to put out ideas that MIGHT be true, and are interesting to think about, but might NOT be true. Pay attention to his qualifying words, like MIGHT, and COULD BE, POSSIBLY, PROBABLY, MAYBE, etc.

It would be lovely to hear whatever he thinks worthwhile to share, WITH the qualifying words highlighted so no one gets the wrong idea. It would be exciting to hear the thought process and, who knows? Someone around here might just have some nugget to add that could lead to a breakthrough.

Thank you!!

 

[frozenborderline]

Ron really laughed at that. He said, " Yeah, my books are only 2-3 pages!" He doesn't often laugh out loud in a belly laugh. You did it!

Hi, I just wanted to check in to see if the OMF is still taking and responding to email correspondence about CFS! I know it must be exhausting responding to everyone's pet theories, but as the science starts to get clearer and clearer, which I think it is, people will want to try stuff/try out theories about how to affect pyruvate oxidation/the kreb's cycle, etc... even if the underlying etiology isn't fully understood

 

[frozenborderline]

It would be lovely to hear whatever he thinks worthwhile to share, WITH the qualifying words highlighted so no one gets the wrong idea. It would be exciting to hear the thought process and, who knows? Someone around here might just have some nugget to add that could lead to a breakthrough.

Thank you!!

i second this. and for those of us who are seeing good CFS doctors who are willing to experiment, having nuggets of insight is always great

 

[Janet Dafoe]

Hi, I just wanted to check in to see if the OMF is still taking and responding to email correspondence about CFS! d

The best way to get Ron messages is through me. I can't read through all the threads, but I try to respond to PMs, to PMs on twitter, and to msgs that tag me. I don't get all of them though. I always forward your ideas and references you send to Ron. He really appreciates them. Like I've said before, he always says, "Who knows where a good idea will come from?!" He has used many of your ideas and they have helped. There are often a lot, and I have a lot going on, but I try to get to them. If i'm not responding, PM me. And don't be offended if I don't respond fast. I have a lot to do. But I really like doing this and I do as much as I can.