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samman1994

Biochemistry section addition?

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Hello,

I wanted to make a suggestion for a section to add. Under life sciences, we have bio and medical, and under physical sciences we have chemistry, but we don't have biochemistry anywhere. Now one could argue biochemistry might be considered a interdisciplinary subject, but I'd say it stands alone. Bio can include everything from literally just bio, to marine bio, to zoology, to vets (although that might be more medical), to even maybe cell or micro bio. As it stands now, it's also the only place for structural, biophysical, computational, theoretical, bio-organic, etc. sections as well. All the sections I just stated have components of bio, but they also have components of physics, chemistry, and computer science as well, so I don't think it would be accurate to ask questions regarding those sections anywhere really.  As it stands, there aren't that many posts in the Bio section anyways, and the community is relatively small compared to some of the other subjects, so it isn't really a big deal, but I thought it might make things a bit more organized and help people address their questions to the right area. 

Just a thing on the side to indicate why biochemistry should be separate. Some schools actually group Chemistry with Biochemistry, and Molecular/Cellular with Bio. Others group Biochemistry with Molecular/Cellular, and others just have Biochemistry and Biophysics separately. I say this just to provide further evidence that Biochemistry is a stand alone subject and is usually almost never grouped in with Biology, if anything it is grouped in with Chemistry. 

Edited by samman1994

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@Eigen, @TakeruK, as the mods whose expertise is in the most closely related fields, thoughts? (For the record, the two main questions here are whether there would be enough traffic to merit a new subforum, and whether it's clearly enough delineated that people understand what goes there and what goes elsewhere.)

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To me all of the areas mentioned (structural, physical, computational, theoretical and bio-organic) fall squarely under either biology or chemistry. 

Biochemistry can be under either biology or chemistry, but is rarely a standalone discipline. I think making another section for it splits up discussion, and I would honestly be more in favor of fewer sections than more.

I think a separate forum for biochemistry especially isn't great, since so many of the program's cross into chemistry or biology that the breadth of perspectives is useful. 

For those that don't know, I'm a biochemist that has been in both biology and chemistry programs. 

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The reason for my post is exactly that, sometimes my posts applied to both chemistry and biology and I didn't know where to ask it. I understand keeping it small though, as stated, it is already a pretty small section relatively speaking, splitting it up would only make it even smaller. That being said, I would not say computational or physical fall under either biology or chemistry. If anything it closely resembles physics and computer science (most people I know in computational labs are usually  computer science majors). Structural biology also doesn't really fall under either category. Sure a little bit under bio, but if its purely structural bio, even if they do DNA and RNA folding/structure (and not proteins), normal bio classes never discuss that, and normal bio labs rarely even do that (they do colabs with structural biologists if they really need the structure of what they're working). Theoretical most closely resembles mathematics and physics (which if you look at the field, there are mathematicians in the biochemistry department for that specific portion). Bio-organic is primarily chemistry. That being said, computational, theoretical, and structural biology all fall under biophysics and structural biology. A standalone department almost every single major school (with a good NMR facility) has. But the broader category for biophysics and structural biology is Biochemistry. 

I am curious why you believe it is rarely a standalone discipline. Almost every school I have seen has a specific major for Biochemistry (undergrad) and most grad programs that would be structural or biophysical, are titled Biochemistry PhD/MA. Schools have entire Biochemistry buildings and departments dedicated to its research, and entire Biology buildings dedicated to bio research. I am a chemist who transitioned into biochemistry. I have worked in both chemistry labs, biochemistry labs, and for a brief period of time, bio labs. So I understand, some aspects of biochem fall under bio (especially anything involving DNA repair) and some under chemistry (especially Bio-organic or synthesizing peptides), but the majority don't really fall under either category (binding of DNA to proteins, structure and function of membrane proteins, allostery in its entirety, DNA/RNA or protein folding and dynamics, anything regarding structure using NMR, xray crystal, CD, etc., anything computational or theoretical, etc.). Again, I understand if you want to keep it all under bio, so I'm not really pushing that, but I definitely do think it is a standalone discipline. 

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You're looking at this too much from a major perspective, which is primarily branding. Most graduate biochemistry degrees come from med schools, and there are increasing numbers of undergrad biochemistry programs. 

But most of these programs don't have many stand alone faculty- I teach in a biochemistry program, and all of us are either chemists or biologists. 

3 hours ago, samman1994 said:

But the broader category for biophysics and structural biology is Biochemistry. 

And traditionally, the broader category for biochemistry is chemistry. It's only recently that it's been subsumed into some molecular bio programs, but the vast majority of the people who teach it are in chemistry programs, from chemistry programs, or affiliated with them. Biochemistry is one of the 5 main subfield said of chemistry. 

If we're being correct about it, the subfield that usually takes in structural biology is chemical biology, which is a biology subfield, distinct from biological chemistry and biochemistry which are part of chemistry. 

3 hours ago, samman1994 said:

binding of DNA to proteins, structure and function of membrane proteins, allostery in its entirety, DNA/RNA or protein folding and dynamics, anything regarding structure using NMR, xray crystal, CD, etc., anything computational or theoretical, etc.

All of these are traditional areas of study within chemistry, bringing home the point that a lot of this discussion fits within the biochemistry-as-chemistry sub discipline. 

I think the perpetuation and growth of biochem undergrad programs (purely for student popularity, most of the time) drives home the idea to many of my students that biochemistry is a standalone discipline, which it's not anymore than ecology or organic chemistry. 

A discipline is predominately defined by the way you think about problems. Biochemistry, as other chemical disciplines, comes at problems from a molecular perspective, as driven home by the techniques you mention above. It's the application of basic chemical principles and techniques to biological systems. 

As to most schools having degree programs titled biochemistry, that's not what makes a discipline stand alone. Most of those degree programs are within a larger department, and that department represents the discipline. There are some biochemistry departments, almost exclusively in medical schools, and they tend to be the exception due to the school lacking a broader chemistry program for them to fall under. 

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By that definition all these questions should be addressed to the chemistry section, but most chemists no absolutely nothing about the above mentioned topics. Why? Because chemistry is primarily aimed towards synthesis. Even most of the physical and analytical is aimed towards small molecules, and thats where the main difference arises. Chemistry is small molecule (whether that be using NMR, HPLC, fluorescense, etc.) and Biochemistry and biology is aimed towards macromolecules. 

My definition actually has very little to do with the majors and more with the research labs and industry. Those define how the major is set up. As someone who worked in the biochem department (with faculty), the major was created at my school since neither biology nor chemistry properly dealt with a lot of biochemistry problems within the field. One needed to take a lot of Chemistry classes, and a lot of biology classes, but there was no need for most synthetic classes or even inorganic for the chemists that wanted to go into Biochem. To that end, I've looked at faculty from over 50+ schools now in the biophysics and structural biology department for my PhD program, and the main field that dominates is Biochemistry. Now there are plenty of Chemists and Biologists, along with a few physicists and mathmeticians/computer scientists, but the majority are biochemistry. 

Yes, biochemistry is biological problems with an approach from chemistry, but also approaches from biology as well. Western blots, footprinting assays, sds-page gels, these are not chemistry techniques, but molecular bio techniques. Biochemistry incorporates in vivo testing as well, which one could say is almost entirely biology. If I were to define Chemistry, it really would be using chemical approaches to small molecules. Biochemistry would be defined as using chemistry and biology techniques towards macromolecules. This is primarily how most people define the fields, and by most people, I mean people's research labs and the industry. 

By the way, just to make sure I am understanding you right. Then by that logic, physical chemistry is really just physics (using physical approaches to small molecules) and physics is really just math (using mathematical approaches to physical life problems), computational Chemistry is just computer science (using a computational approach to solve problems), etc.

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You seem to have a very narrow definition of chemistry. And I'm not sure you understand how I applied my definition. Chemistry in no way biases towards small molecules- it biases towards a molecular basis for understanding how things work. There are a number of fields that study immense molecules, including biochemistry, that are part of the field of chemistry (not to mention materials chemistry, polymer chemistry, supramolecular chemistry, etc.).

24 minutes ago, samman1994 said:

Why? Because chemistry is primarily aimed towards synthesis. 

This, to me, indicates that you have a very narrow view of the field of chemistry, although you seem to feel you have an awfully deep understanding of how large fields of study should be organized, and from what I recall you haven't started your PhD yet? I get you have a very specific definition and feel or what biochemistry is, but I wouldn't say it's by any means universal. I don't think any of my colleagues would feel they aren't chemists, and I certainly don't.

The way you talk about things working is the way some schools are organized, but I wouldn't say it's the majority. It's also a new organization that comes not from, as you say, research labs and industry, but driven by what students think they want to major in. Biomedical areas are popular, so schools organize degrees around them. 

Research labs and industry, not so much. 

Finally, I think you'd be surprised at how many of those topics chemists are familiar with. I will happily answer questions on those areas- my research group studies all ranges of nucleic acid chemistry, and I've got close to 7 years of experience running cell culture labs and training people in that area. Biochemistry is one of the 5 major subdiscipline of chemistry (organic, inorganic, analytical, physical, bio), and most chemists have probably taken biochem at some point  

I think you could also ask many of your questions in the biology forum, and get good information. My bet is that many of us read/check on multiple subdiscipline forums, and you'll get answers wherever you post. 

Finally, you mention techniques like PAGE- it was developed by a chemist (a biochemist), and won the chemistry Nobel prize. Tiselius very clearly considered himself a chemist his entire career. Edward Southern, who was the progenitor of the southern blot (from which other naming is pulled- western among them) was also a chemist. Footprinting assays are also generally considered a chemistry technique. Their use in biology is what gives rise to the field of molecular biology, using molecular (chemistry) techniques to study biological systems. 

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My interpertations come primarily from my observation to how most schools have their systems organized, working in the industry, and from those in the field around me I have not yet started my PhD yet, I am still looking at potential schools. In regards to the knoweldge of Chemists, i worked alongside many Chemists ( as well as majoring in Chemistry). I understand you're point of view and approach, I am just saying, that is not what I have seen and experienced in my time in Chemistry. Very few chemists, from my experience, know anything outside of small molecules. Chemistry is of course a huge field that deals with larger molecules (especially when it comes to engineering synthetic membranes or even sometimes extended to how small molecules interact with proteins/enzymes). However, that is usually when I start to group it to Biochemistry. When I was in a synthetic lab, we synthesized natural products, then tested their binding with certain proteins using ITC. However, if my PI were to define our field, it would be synthetic chemistry with aspects of Biochemistry (primarily the binding studies done with proteins). Again, my knowledge of the field and how it should be separated comes primarily from my experience, looking at different schools, working in different labs, and working in the industry. From my understanding (and those I have worked with), chemistry is primarily small molecule, and biochemistry is macrmolecules. 

Now there could be different definitions to the field, but this is how my department and school/faculty (chemists and biologists) defined the field. As stated earlier, I was part of the process of creating the Biochem department exactly for that definition. In a way, this isn't even really my definition for it, it was from those I have worked with, and I thought it made sense. That idea has only been solidified by my experience in industry, as well as looking at various research programs across the country. Again, I'm not saying you're wrong, just that I haven't really seen it defined that way from my experience. I am in no way in an expert in the field (Chemistry or Biochemistry)

Edited by samman1994

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You keep saying biochemistry isn't chemistry... By defining biochemists as different from chemists. If you group biochemists in with chemistry, then your point becomes more that organic chemists aren't biochemists. 

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I think Biochemists are chemists, but they are also biologists too in my mind. I see biochemistry as taking aspects of Chemistry, Biology, and Physics, but I don't see it as taking any more of one particular group. Hence, why I think it's its own discipline that borrows from the other disciplines. I look at it this way: I find it incorrect to call a physicist a mathametician. I mean, it's not wrong, but they're really a physicist. I look at calling a Biochemist, a Chemist or a Biologist, improper as well. I mean, you're not wrong, but I think the more proper term is Biochemist, because I see it as it's own independent field. When I do go to a PhD program, and do join a structural biology/biphysics lab, I would end up telling people I'm a Biochemist, not a Chemist or Biologist. 

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So why is that any different than a physical chemist, who takes aspects of physics and aspects of chemistry?

Biology and chemistry aren't that fundamentally different of disciplines. But they are very different in training. Chemists build up from molecules to larger things, biologists build down from ecosystems to molecules. 

By and large, biochemistry approaches studies the way chemistry does. This is especially true because biochemistry is a really young field, made up predominately of chemists. 

Biochemistry builds on organic chemistry and physical chemistry to explain why things we observe in biology happen. That doesn't mean it's drawing heavily on biology, it means it supports biology. 

Taken another way, he study of biochemistry doesn't require background knowledge from biology. Sure, that can help- but it isn't necessary. I would let someone take my biochem course if they haven't taken intro biology with the understanding that they wouldn't get all of the applications of what we were talking about. I couldn't let in someone who hadn't taken organic- it's a direct pre-requisite for understanding most of the material in the course. 

Chemistry and Biology are large fields. If you're a biochemist, you are a chemist or biologist as well, likely both. 

Your example of physics and math doesn't fit the same model. Physics uses math, but the approach and perspective isn't the same. 

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I just wanted to add some older discussion this topic- namely the flury of opinion pieces written in 1986 after a lecture at the Royal Society when it was suggested that biochemistry was irreducible to chemistry. The response from Perutz in New Scientist is worth reading (1986, 1528:36, page. 36 in the link below):

https://books.google.com/books?id=OthdH0JQGiYC&pg=PA1&dq=New+scientist+1986+1528&hl=en&sa=X&ved=0ahUKEwip2Zzo-ubVAhWXxIMKHWLsADoQ6AEIMDAC#v=onepage&q=New scientist 1986 1528&f=true

as is the article from Steven Rose in Cell, on reductionism that cited both the talk and Perutz's piece. 

http://www.cell.com/trends/biochemical-sciences/abstract/0968-0004(88)90138-7

Much of this comes down to reductionism. Is it better to define hundreds of small, fractured disciplines or realize they're mostly part of a few larger ones? I take the latter view. Broad training tends to be more valuable than narrow training. I teach in, and am helping to develop a biochemistry program, but I wouldn't recommend students who want to go to graduate school in biochemistry major in it rather than chemistry. It's more intended for pre-med students who need reduced course requirements and flexibility, and sacrifices depth on the fundamentals. Focusing on one "application" rather than the fundamentals is, I feel, more detrimental to research than a gain. 

It's why I call myself a chemist that works in the area of biochemistry rather than a chemist. Some of my colleagues are biologists who work in the area of biochemistry. But I don't know many who identify solely as biochemists. Not saying people don't, but it's just not something I run across much. 

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I understand. Although I think it really depends on the program. As someone who has majored in Chemistry and is now going into "Biochemistry" programs, I really wish I had majored in Biochemistry. I know a lot about synthesis, I could probably name over 20 different techniques just to make a Carbon Carbon bond, but I know nothing about biology. I know nothing about transcription, translation, post-translational modifications, glycosylation, cloning, sequencing, genes, etc. I could go on. I have taken Biochemistry for a year for my undergrad, but that did very little to help address these issues. When most research labs are looking for how do proteins interact with DNA, how does that effect diseases or transcription? How does RNA structure effect translation, what proteins are involved, how is that involved in disease, etc. My Chemistry background helps answer absolutely none of these. Getting a job in the industry is equally as difficult. They want someone with experience in cloning, immunotherapeutic techniques, anti-body  work, FACS, ELISPLOT, Western Blots, etc. All techniques that I lack because I never took bio. This is why I hold the opinion I have. As someone who majored in Chemistry, almost all of it has been useless when it came to industry/academia in biochemistry. Sure the organic helped me a little bit, but all the synthetic classes I took havn't helped at all, inorganic hasn't helped, etc. Chemistry majors (from school programs I have seen), focus primarily on synthesis, and nothing on bio (this may also explain why my department and myself have the opinion we have of the field). Biochemistry, focuses on a nice mix of the 2 that will become incredibly useful in trying to find a job in biochemistry, and a lab. You have the molecular, cell, and genetic background, but also the organic, analytical, and physical background of chemistry. 

Interestingly enough, at most of the conferences I've been to, I've seen plenty of people state they are biochemists. In fact, the people that did call themselves chemists were almost exclusively synthetic (polymer, material, surface, etc.). The ones who worked on theoretical or computational said they were either theoretical or computational chemists or biochemists depending on what they were working on (small or large molecules). Out of curiosity, I wonder if this is a regional thing, where do you work? My experience with conferences and work is primarily from the West (California, Oregon). 

Edited by samman1994

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Not regional in my experience. Seen it in the west, northeast, midwest, and south, and at national conferences.

I think perhaps you're just a bit overwhelmed. Most of what you're talking about you may not remember (although I cover most of it in y biochem classes), and it's pretty easy to pick up reading during your first year.

Most of what you're talking about seems to be specific to you and your programs. 

Where I've taught (and interviewed) those are all techniques you'd cover in your year of biochem. Similarly, I would assume if that was someone's interest they'd do research in biochemistry for at least a few years, where you would likely pick up a lot of the rest. Maybe you just had a really unusual chemistry experience, but I'm really surprised that two semesters of biochem with labs didn't prepare you for talking about protein-DNA interactions or RNA folding. 

As to your last statement... Saying you're a theoretical chemist is saying you're a chemist. That studies theory. It's like saying you're an organic chemist. I think a lot of people feel the same way about biochemist. It's a type of chemist. 

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I'm too far removed from Biology/Chemistry to really appreciate or understand the nuances of the discussion "Is Biochemistry part of Biology, Chemistry, or something else?"

But I think when determining whether or not to create a new subforum, I think assessing whether or not there is a need/demand for the subforum is more important than whether or not X is distinct from Y or Z. As @fuzzylogician and @Eigen mentioned at the beginning, there is consideration of whether or not it would split the discussion too much.

I took a quick look at the Biology and Chemistry subforums. 10 threads in the Biology subforum have been posted in since August 1. 2 threads in the Chemistry subforum have been posted in since August 1. To me, this doesn't seem to justify the need to separate out the Biochemistry from the 12 threads that have been active since August 1. That is, a biochemist should be able to click on both subforums and find any biochemistry threads without having to read through too much. 

I am also of the mindset that we should have fewer subforums not more. For example, I would personally make an argument to group all of the basic sciences into one mega-forum! When I first joined, there were not very many forum tools to track threads and to search for them (and I joined years after TheGradCafe began). So I think back then, it made more sense to have discipline specific forums that users can choose to follow, or that you can scroll through and click on the ones with the "new posts" logo. But now, there are so many ways to customize multiple feeds that show updated information that browsing threads by forum is a little obsolete, I think. For example, a feed returning threads containing the string "biochem*" could easily help a user pick out the related posts!

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