Posted by: unlikelygrad | October 7, 2014

What hydrogen peroxide does to your body

I cringe every time a friend of mine posts an article like “25 uses for hydrogen peroxide” on Facebook.  Usually these are the same friends who rant about the evils of ethylparaben, propylene glycol, or the like.  Well, I’ve spent the last 5 years learning what cells do with hydrogen peroxide…and what it does to cells.

Executive summary: Honestly, people, hydrogen peroxide is much worse news than propylene glycol.  I would not brush with it, gargle with it, or even put it on cuts.  Yes, it kills germs.  But why? Because it can do serious damage to ANY cell.  Including yours.

* * *

Now here is the science behind my statement. Your cells always have a small amount of hydrogen peroxide in them, for two reasons. The first is that cells actually use hydrogen peroxide to “digest” fats into smaller particles.  They do this because… drumroll… hydrogen peroxide is good at breaking down fats.  Did you know that your cell membranes are also made of fats?  Yes, in high concentration hydrogen peroxide will break your cell membranes.  It does that to germs, too, which is why it is such a good disinfectant.  Obviously, your cells don’t want to kill themselves, so they use hydrogen peroxide in a very specialized part of the cell (an organelle known as a peroxisome) so it can’t impact the rest of the cell.  And all around the peroxisome, there are specialized enzymes–catalase and peroxidase–designed to break down hydrogen peroxide and keep it from getting out to the rest of the cell.

The second reason that cells have hydrogen peroxide revolves around what we chemists call ‘the four electron reduction of oxygen to water’–what biologists call respiration.  As oxygen is reduced (gains electrons) it passes through four intermediates known collectively as reactive oxygen species (ROS).  These intermediates are known as superoxide radical, hydrogen peroxide, and hydroxyl radical. (For plants, the reverse reaction, photosynthesis, is even more strongly implicated in ROS production.  Having done a lot of work with photosynthetic critters, I understand the photosynthetic ROS production pathways  a lot better than I do than those linked to respiration.)

Normally there are enough electrons around that the reaction goes all the way to water, but there are enough “leaks” in the system that (usually) superoxide can get out of the pipeline and into the cell.  This is why there are plenty of enzymes around the mitochondria and chloroplasts–superoxide dismutase to break down superoxide (and turn it into hydrogen peroxide) and catalase and peroxidase to break down the hydrogen peroxide.  The damage is contained.

It should be noted that of the three ROS produced by respiration, superoxide is highly reactive and can do lots of damage; hydrogen peroxide is the least reactive; and hydroxyl radical is the most reactive and toxic.  Superoxide and hydroxyl radical, especially the latter, are the most common “free radicals” implicated in cancer, as both can irreparably damage DNA.

So what about hydrogen peroxide?  Well, even though hydrogen peroxide is less reactive than the other two ROS, (1) it is still capable of doing damage; and (2) if it meets up with any metals (and you can find those in the cell in small concentrations, as they serve as the basis for many enzymes) it will react to form the highly reactive and damaging hydroxyl radical.  That’s why the cell is so intent on keeping hydrogen peroxide low–not just because it can do damage itself, but also because it can turn into a highly toxic radical species.

* * *

Let’s go back to the uses for hydrogen peroxide you frequently see proposed on the net, like using it as a mouthwash. There are several problems with this. First of all, hydrogen peroxide can diffuse through the cell membrane.  If you were to gargle with a reasonably concentrated solution of superoxide, it would damage every cell membrane it came in contact with, but that’s it.  Superoxide is a charged species and therefore doesn’t go through the cell membranes very well.  But hydrogen peroxide, which is both electrically neutral and similar in size to water can easily pass through the aquaporins designed to let water through the cell membrane.  So it gets inside your cells.

But so what?  Aren’t there enzymes designed to break it down?  Well, yes there are, both inside and outside the cell. However, kinetics must be taken into account.  CONCENTRATION MATTERS. The more hydrogen peroxide there is, the longer it will take for the enzymes to break it down.  The hydrogen peroxide in  your cells is usually present in nanomolar concentrations; the hydrogen peroxide you buy at the drugstore is just a bit under 1M in concentration.  So you are hitting your cells with roughly one billion times the amount of hydrogen peroxide they’re used to dealing with!

* * *

In short–hydrogen peroxide can damage your cells in the same way it can damage germs.  I would not use it topically and I particularly would not consume it in any fashion. It’s ok to use it for a disinfectant on non-living items, but be sure to rinse well with purified water to get rid of any residues. (There’s a reason hospitals use alcohol as a disinfectant instead of peroxide–it evaporates quickly, leaving no residue behind.)

 

* * *
Edited to add: I have been asked for my sources.  The most comprehensive source for this sort of material is “Free Radicals in Biology and Medicine” by Halliwell and Gutteridge.  I think they’re on 4th edition now?  It’s a textbook, but it is far more understandable to ordinary folks than scientific papers.  It’s become my Biology Bible for writing my dissertation.

At some point this will be revised to be even more scientific and will include many more sources, but I’m not likely to get around to that until I’m writing my dissertation intro, which will cover a lot of hydrogen peroxide cellular biology (among other things).

 

Posted by: unlikelygrad | August 31, 2014

The last year of grad school…

…is kicking my butt.

We’re down to roughly the last 6 months here (last 4 months if all goes well) and I’m working like a maniac.  Luckily, lots of it is writing, which I can do at home or in waiting rooms during my kids’ appointments, etc.  Unluckily, not all of it is writing–the bacteria project is going full steam ahead, which entails occasional overnights in my office so I can monitor stuff every couple of hours for 24 straight hours.  I hope to have all of the lab work done by the end of October.

Despite working way too much, I somehow have time to keep an eye on the job market.  My resume and CV are updated, so hopefully I can take either the academic or industry route.  I would prefer academia, of course, but my primary goal is to remain in the Denver area until my kids turn 18.

The stress is taking its toll on me.  My immune system is weak, so I get sick often; and my vision is going downhill at an alarming rate.  (Just went to the eye doctor and left with a prescription for…gulp…bifocals.)  I have to finish before it kills me.  Literally.

Posted by: unlikelygrad | August 15, 2014

why I post about depression

I first experienced depression during puberty, maybe age 13 or so.  It made me unhappy at first; by age 14 I was downright miserable, and by 15 I was suicidal.  Not once did I ever think of getting help.  Why not?  Because, obviously, if I was suicidal, there was something wrong with me.  I mean, really, only the hopeless cases get suicidal!

At age 16 1/2 I left for college, still quite depressed.  At the highly competitive and very stressful university I attended at first, I failed classes.  This did not help.

After I dropped out of that school and got married (age 18), I spent a semester in community college, trying to raise my GPA enough that I could apply to another university.  While I was waiting in line to register for classes–it was a long line, and it moved very slowly–I picked up a school newsletter to read.  One article was about how to know if you had depression.  I looked down at the list of symptoms–they almost all applied–and almost started crying, because suddenly I knew.  I was not horribly bad: I was sick.

I wish I could say that I got help right away, but I didn’t.  When I went home and told UnlikelyDad, he quickly shut me down: “Nonsense.  Everyone gets blue now and then.”  And so I didn’t do anything about it.  But I knew, and knowledge is a powerful weapon.  Over the years I learned things that helped me manage the depression–a healthy diet, exercise, etc.  After my second bout with suicidal thoughts, I went to the library and got a book on Cognitive Behavioral Therapy, which was very helpful.  (By this point, UnlikelyDad was no longer openly against therapy–but he refused to let me have the money to go to therapy, which our insurance didn’t cover, or use of the car to go to therapy.)

Things got better when I got to MyU and could visit the counseling center.

Things got better still after I was diagnosed with PTSD and referred to a trauma specialist who helped me work through the emotions attached to the past abuse.

Things got even better after I went on medication.  (One of my initial worries about going on meds is that I would forgot to take them on a regular basis.  I have to admit, I still do forget after all of this time–but it’s still a huge help.)  I was on Celexa at first; switching to Lexapro got rid of the side effects that made me hate meds in the first place.

Things got even better still after I got a protective order that severely limited UnlikelyDad’s ongoing harassment.

The final piece of the puzzle was a new cognitive behavioral therapy technique that my therapist introduced this summer.

For the first time in…my whole life, maybe?…I feel…normal.  I think.  Is this what normal feels like?

I wish I hadn’t waited until almost-40 to get help.  I wish I could have felt like this in my 20’s.  Don’t get me wrong, I’ve accomplished a lot in my lifetime, but I can’t imagine how much more I would have accomplished had I not suffered from depression.

I blog about depression because I want others who suffer from the disease to know that they are not alone.

I blog about depression because I want people to know that there is hope.

I blog about depression because it is treatable.  Even if you can’t take meds (I have a friend who’s had bad reactions with all of the meds he’s tried), there are things you can do to ameliorate the symptoms.

I blog about depression because I want others to get help.  To everyone who’s out there feeling like you don’t have the mental energy to get out of bed…who feels like you are worse than a lowly worm, because at least worms are good for the soil…who mires in the blackest abyss of depression…THERE IS HOPE.  Please, get help.

Posted by: unlikelygrad | August 12, 2014

on the social unacceptability of depression

In the aftermath of Robin Williams’ suicide, many people are posting about depression and how to help people who have it and how to reach out and ask for help if you are depressed yourself.

As someone who’s suffered from depression on and off for much of my adult life, and part of my pre-adult life as well, I think that most of these people have no clue what they’re talking about.  It’s hard enough for someone who’s depressed to reach out for help, just by the nature of the disease.  But society makes it even harder because of the nature of our modern culture.

In modern America, and (I imagine, anyway) much of the western world, it is not socially acceptable to have any “negative” emotions in public.

Examples:

  • If someone asks me how I’m doing and I say, “OK,” they say:  “Just OK??!!”  There’s an element of surprise, because the only socially acceptable answers to that question are “fine” or “great”  something of that ilk.  And God forbid I should say, “Things aren’t going so great right now.”  (I always try to answer this question honestly and people look at me like I’m growing a third eye when I say anything remotely negative.)
  • People apologize, all the time, for being sad about appropriately sad things.  For example, in Allie Brosh’s interview on Fresh Air she apologizes repeatedly for getting choked up when she talks about the period where she was suicidal. (BTW, if you haven’t read her essay on depression, you ought to.) I’m sorry, but that sounds to me like a very scary period of one’s life and something that one ought to have strong feelings about.
  • Another apology story: I was having lunch with my mother-in-law one day (back when I was married).  She was talking about her mother’s Alzheimers, which had gotten much worse that year, and started crying.  Of course she immediately apologized for crying in public.  I told her, “Look!  Your mother has been suffering from a horrible disease, and now she can’t remember you, and she’s dying!  It’s sad!  You do not need to apologize for crying about it; go ahead and cry!  It’s healthy to grieve!”  She was a little taken aback, but grabbed a Kleenex from her purse and proceeded to cry even more.  But she couldn’t stop herself from apologizing again.

I look back at my own life, at my own depression, and see this pattern.  I wanted to reach out for help, but I couldn’t, because God-only-knew how they would react if I told them how I was really feeling.

During the second period of my life when I considered suicide (the first was when I was a teen), I had some close and caring friends who tried to check in with me often. They knew, by that point, that I was married to an abusive man who limited communication, and I would let them know what was going on via my LiveJournal account (which he didn’t know about at that point–he hadn’t yet started tracking my every move on the web).

One day, I left the house with the specific intent of committing suicide. It didn’t happen.

When I came back, this is what I wrote for my friends to read: “Today I was depressed. Really depressed. Really really depressed. Really, really, really…well, you get the picture. So I went on a walk.” Then I talked about something traumatic (that happened to someone else) I had witnessed while out on the walk. Then I said: “So maybe my life isn’t that terrible after all. Bad, yes. But not terrible. I came home and hugged my kids extra tightly.”

No mention of suicide. No, God forbid that I should ever tell my closest friends that I wanted to do myself in, that I had a plan of how to do it, that I went out intending to put that plan into action. In fact, I didn’t tell them that was what happened that day…for a good 6 years after that incident. Because even a person like me, who is socially unacceptable enough to reply “not too great” when someone asks me how I’m doing, knows that the fewer negative emotions that are brought up in public, the better.

There is nothing wrong with being sad. There is nothing wrong with being afraid. There is nothing wrong with grieving. There is nothing wrong with being angry for a good reason (like finding out that your kids were endangered). It is bad when people let negative emotions like fear completely govern their lives, but the feeling and expression of these negative emotions is not wrong. It is time that society understands that and acts on it.

Until that happens, depression will remain a hidden disease and we will be caught off guard every time a celebrity commits suicide.

Posted by: unlikelygrad | August 6, 2014

doing the shuffle (or trying to)

The year I started at MyU was the year the administration also decided to increase the number of undergrads.

MyU is a tech school, so all students are required to take chemistry, physics, and calculus–generally in their freshman year.  Needless to say, a 25% increase in the number of incoming freshmen impacted the chemistry, physics, and math departments pretty heavily.

The following year (with even more freshmen expected), the chem department significantly increased the number of grad students they admitted so they’d have enough TAs to handle chem labs.  At the end of the year, they realized they had a significant problem–it was hard to find labs willing to take in all of the students.  Of course, this was all happening about the time that a number of professors were retiring.

During my third year they hired two tenure-track professors and one teaching professor.  They also hired another tenure-track professor jointly with another department.  My fourth year they hired another teaching professor.

This last year, my fifth year, they hired yet another teaching professor and one more tenure-track professor to start this coming fall.  The new TT prof is our former postdoc, PatchyGenius.

It’s been interesting having PatchyGenius as the incoming prof because I’ve gotten a glimpse into the politics of hiring a professor in a growing department.  The real problem is that while the department is growing, the space allotted to it is not.  So where will PatchyGenius go?

One of our professors, Dr. Catalyst, is transitioning into retirement.  He still teaches half of the year, so he still needs an office.  Last year the department moved him from his big office downstairs to a smaller one near my lab.  Now, it appears, he is vacating his smaller office for PatchyGenius–but where will the administration put Dr. Catalyst now?  (He teaches organic and, as a result, has the best-attended office hours I have ever seen.)  In any case, PatchyGenius will be set for an office. (Or so we assume; we’ve seen Dr. Catalyst moving his stuff but no one has officially told PG that the vacant office will be his.)

But now he needs lab space.  And spare lab space is something we do not have.  There were rumors that he would share a lab space with one of the new hires of my third year; unfortunately, the folks who currently share her lab space belong to a different department in the same building, and it isn’t kosher to take over lab space that isn’t allocated to chemistry.  Then there were rumors that the Hand-Waver lab would be sharing a different lab space with PatchyGenius, which would have necessitated shuffling two other lab groups to new areas.  I think I’ve heard a total of four different possible lab rearrangements, none of which have been approved yet.

So Patchy Genius has officially started as a TT prof–the beginning of the school year is less than two weeks away–but still has no idea where he will be working.  He’s still crammed in the post-doc office with five other people.  In the mean time, Dr. HW has kindly allotted him his old counter space in our lab–where he’d worked the last two years–to run a few small experiments.  Midnight, the undergrad who did research with him before, will be returning as his grad student.

It’s getting a bit crazy here.

Posted by: unlikelygrad | July 16, 2014

A tribute

People always tell me that they’re impressed by what I’m doing–going to grad school as a single mom with four kids.  I’m not saying that’s nothing–but it’s nothing compared to my best friend.

C was a single mom until a couple of months ago. She has four kids: two biological kids from her failed marriage (both adults as of last year) and two kids (her biological grandchildren–which is scary since she’s my age) adopted after her divorce.  Both of the younger ones have mental and physical health issues.

Despite this, she’s also a grad student (currently working on her M.S.N.,  going for her D.N. in the fall).  She was working as an E.R. nurse until a couple of years ago, when she was in a serious car crash that left her with brain and spinal injuries and severely restricted her ability to lift.  That ended her career as a duty nurse.  Last year they attempted to fix her cranial/spinal issues with a major surgery…in the middle of the school year.  She ended up getting a B in one of her classes instead of an A.

Last month, after a rather severe recurrence of symptoms, she was scheduled for another surgery.  They just finished that half an hour ago, after 10 hours in the OR.

C is one of my heroes.  She’s smart (despite memory impairments), sassy (but loving), nerdy (“Here, let me show you my MRIs and explain them to you!) and doesn’t know how to give up.  Having her in my life has been a blessing.

Posted by: unlikelygrad | July 15, 2014

4 1/2 girls in one room

A couple of days ago we had a meeting to discuss some final changes to an about-to-be-submitted paper.  This paper has four authors, and all four are female.  One (our collaborator from New England) couldn’t be there in person–she’s the half-person alluded to in the title.

The four whole girls in the room were me, Dr. Hand-Waver, MacGyverina, and Baby MacG.  MacGyverina, who’s working half-time right now, has arrangements for Baby MacG for the two days a week she’s in lab; the rest of the time she tries to work from home.  The meeting fell on one of her at-home days, so she just brought the baby with her.

Dr. HW was busy explaining one of the issues to us when she stopped, looked at the two other adults–who were playing peekaboo with the baby–and asked, in frustration, “Are you listening to me?”  We assured her that we were.   She had a dubious look on her face, but finished explaining the issue anyway.  Then she punted the discussion to me.

And then, not five minutes after she’d all but chewed us out, I caught her making goofy faces at the baby as I tried hashing out the issues I had with our discussion session.

Needless to say, it was a highly amusing (and very informal) meeting.

Posted by: unlikelygrad | July 2, 2014

dragggggging on

Dr. Hand-Waver found money to keep MacGyverina on through the summer–which is good, because we encountered a Crisis of Epic Proportions with our diatoms last spring and we didn’t get all the data we needed for our joint project.  MacG came back from maternity leave a few weeks ago and we are diving back in.

In the mean time I’ve also been working on my last project, which involves bacteria.  Bacteria stink and so do their assorted growth media.  I had to start out by making growth curves which, unfortunately, involved taking readings every 2-3 hours for ~40 hours.  This involved sleeping at school (in a sleeping bag on the floor of my office) for 2 consecutive nights.  (I had to time the growth curve so that it didn’t interfere with my parenting time.)

At this point the Pacific Paper is with our collaborator, waiting for her final input before submission; and the astrobio paper is hopefully in its final form and ready for submission (my parts are done for sure), though I think some of the other co-authors had a bit of feedback.  It seems like the more authors you have on a paper, the slower the revisions go.

At this point my goal is to defend my dissertation in December.  Hopefully my experiments will all go as planned from here on out…HA!

I’m getting pretty sick of grad school.  I am sick of being poor.  I have thoughts, from time to time, of leaving ABD since I now have enough skills to get a pretty good job.  Unfortunately, what I really want to do is teach at the college level…and I do need to finish my Ph.D. for that.

In the mean time, I frequently find myself watching this video:

Posted by: unlikelygrad | April 10, 2014

Progressing

Today, right after lunch, I meet with my committee to talk about my thesis proposal.  Writing the beast has made me realize exactly how much I have accomplished, even though I still don’t have a first author paper.  (I’m working on it and I hope that that will change soon!)  I was very happy to hear that the “proposal defense” was not an adversarial process.

 

Yesterday I was in with Dr. Hand-Waver, going over my presentation for today, when the provost and the department head stopped by.  Evidently her promotion was authorized yesterday afternoon; she’s now a full professor. So congratulations, Dr. Hand-Waver!!

Posted by: unlikelygrad | March 31, 2014

Welcome little one!

MacGyverina had her baby girl  last weekend!  I went over to the hospital yesterday and held the Adorable One for half an hour.

I always forget how small they are when they come out.  When I picked her up, I asked MacG if she were smaller than usual.  No–she was over 7 pounds.  That’s not small for a newborn, but it is small for a human being in general.

We haven’t submitted our paper yet (still waiting for Dr. HW’s final approval–she’s been swamped and is going out of town this week) but it’s mostly put together.  We’ve even started filling out the submission form.

In the mean time, I’m writing like mad.

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