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comment by mk
mk  ·  4077 days ago  ·  link  ·    ·  parent  ·  post: A farewell to bioinformatics

I'm so conflicted here. This is rant-worthy stuff, and I also agree. Hell, we've paid for these kind of analysis.

I would love to hear some specifics, however. Biology is dirty, confusing, and complicated. I think textbooks do an incredible amount of harm by drawing diagrams of cellular systems as if things actually worked like they suggest. Genes don't do things, and proteins don't have specific functions. Journals love to say that they do, however. Everything is contextual and a part of multiple feedback loops. Bioinformatics can be valuable when applied in that light. However, using bioinfomatics to find parts of an intricate machine is dumb.

I want to know what Fred Ross' expectations are.

That said, most bioinformatics is based on unjustified expectations.





thundara  ·  4077 days ago  ·  link  ·  

I'm curious, do bioinformaticists just not ask the right questions? Are people just sequencing, building (potentially faulty) genomes, tools to depict and search them, and then just abandoning them?

The author of the link did little to give specifics of where scientists in the field were failing, sadly.

mk  ·  4077 days ago  ·  link  ·  

    I'm curious, do bioinformaticists just not ask the right questions?

IMO that's not just the problem of bioinformatics, but much of biology in general. TBH I think some of the language we use in publications is absurd; but, I have been guilty of it. We speak with too much certainty, and don't use contextual terms enough. If you find that a protein does something in one context, you should report that the protein does it in that context. Don't say that is what the protein does, and please, don't name it for the context in which you found it in.

I work with miRNA a lot, and one thing I love about miRNA, is that they each are just given a number. It's so liberating and much more honest IMO.

Thanks for the post, BTW.

thundara  ·  4077 days ago  ·  link  ·  

    TBH I think some of the language we use in publications is absurd; but, I have been guilty of it.

I disagree, sometimes gene names can be a little over the top, but protein names tend to be pretty accurate (Kinase target, structure isomerase, etc) and in general a lot of the language makes sense in the context of the history of the research. Given the precedent already set by past research, I'd say that returning to a flat numbering scheme would be counter-productive and just complicate discussion over them. It's at least easier to add a note when talking about a protein if it's function differs from its name.

Oftentimes researchers come up with pretty new methods / patterns that require new / descriptive names. Yeah, it means you have to spend time learning the language if you want to be able to understand, but wuzzy language hurts communication, and domain-specific vocabulary are pretty common among most research fields (Try reading a math publication with only a bio background).

There is something to say about language duplicated from more general fields (Re-inventing math terms in biology / chem / etc), but that's easy to criticize, but hard to fix, given that scientists will often hide their newest projects from others, preventing them from gaining the comments from more knowledgeable peers on what to call it. Then you just have peer-reviewers as the safety net, and things fall past them all the time.

    I work with miRNA a lot, and one thing I love about miRNA, is that they each are just given a number. It's so liberating and much more honest IMO.

How common is it to have defined functions (Catalysis, binding certain chemistries, etc) when it comes to miRNA?

    Thanks for the post, BTW.

Oh, no, thank you all for the discussion, I love getting to talk with others about hardcore science :D

b_b  ·  4077 days ago  ·  link  ·  

Molecular biology is the real problem, as he correctly states. Too much data with no way to make sense of it. Most studies are devoid of any deeper meaning than just the very specific technique that is reported about. More data collected on better machines is what is considered good science right now. Lots of time and money wasted.

thundara  ·  4077 days ago  ·  link  ·  

Curious, could you give some examples of that? I wouldn't think most (even computational) biochemistry / neuroscience / etc would be considered devoid of any deeper meaning.

b_b  ·  4077 days ago  ·  link  ·  

I am admittedly in the minority of thinkers on this.

Here is how the typical molecular biology study goes these days: 1) We have a disease model. 2) In our model, we have found that gene/protein X is altered. 3) We restored expression/function/activity of gene/protein X to a more physiological level. 4) We were able to mitigate the disease state to some extent.

Most disease models are non-physiological, for starters. Second, and most important, only specific genetic diseases are caused purely by a gene being out of whack. Most diseases are caused by a combination of genetic and environmental factors, and their etiologies are very complex. All we do with most studies is to try to put fingers in the dike. Unfortunately, the grant system and the academic literature system is most well equipped to score these types of studies. NIH wants logic, technical ability, and sensitive measurement, without much regard for utility. Fancy machines make great slides to show Congress. There is nothing more torturous than sitting through a talk where a researcher describes their "exciting new microarray results."

If you want an actual specific example, go to PubMed and just start taking a peek around.

thundara  ·  4077 days ago  ·  link  ·  

I don't follow...sure, a lot of research is medically inspired, but that threads off plenty of research into the entirety of the workings of cells. I'm right now reading about kinetic studies of protein folding as a factor in formation of protein aggregates, which may or may not be linked to a number of diseases, including ALS, Alzheimer's, and drug resistance. Then you have entire pathways of metabolism being studied to aide in nutrition and obesity studies (And vice versa).

    only specific genetic diseases are caused purely by a gene being out of whack

Sure, but you still have larger categories that can be slightly more distantly linked to general diseases. (Ex: Tumor-suppressor genes and cancer)

    NIH wants logic, technical ability, and sensitive measurement, without much regard for utility.

This is where you've lost me, does medical application or biosynthesis not count towards utility?

    If you want an actual specific example, go to PubMed and just start taking a peek around.

Citing one would be preferable, I'd say that the majority of the microbiology papers I've read thus far made sense in some context or another. Some's shite, but higher tiered journals are generally a little better at filtering for that, and who am I to judge if someone's research is worthless? :P

thenewgreen  ·  4075 days ago  ·  link  ·  

I've reached out to Frederick and he said that if anyone has any questions for him regarding this piece they can email him. He seems a nice fella. I'll pm you his email address. If anyone else is interested in asking him a question, please let me know.