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Biology Help Desk Again

Samantha Wright (1324923) writes | more than 2 years ago

User Journal 25

I'm really not sure how long these last as comment-on-able, so here's another one. I'll try to be a little more vigilant in making sure there's always a journal open for asking questions.

I'm really not sure how long these last as comment-on-able, so here's another one. I'll try to be a little more vigilant in making sure there's always a journal open for asking questions.

A little more elucidation: I'm in the fourth year of a combined bioinformatics/medical informatics degree. Most of my semester is from the CS curriculum, but I have gotten through biochemistry, genetics, molecular biology, physiology, and organic chemistry courses. (Mostly in the presence of pre-med students.) I've also taken genomics-specific courses and worked in a molecular biology lab studying C. elegans, and a medical lab studying Autism.

So ask away!

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25 comments

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My question: (1)

Captain Splendid (673276) | more than 2 years ago | (#37923354)

What the hell are you doing here then? Or do you like slumming?

Re:My question: (1)

Samantha Wright (1324923) | more than 2 years ago | (#37924416)

Slashdot has a very diverse user community. Surely that's become apparent long ago? If it's any consolation, most of my classmates are generally Facebook-loving doorknobs just like any other population of college students.

Re:My question: (1)

Captain Splendid (673276) | more than 2 years ago | (#37924882)

Slashdot has a very diverse user community.

Not really. Lots of technocrats, not much else.

Surely that's become apparent long ago?

Actually, it's the other way around. We used to have a diverse, lively and chatty community, but this site's love of stasis drove most of them away several years ago.

And those of us who chose to remain only do so because we're lazy, stubborn or lacking in useful hobbies.

If it's any consolation, most of my classmates are generally Facebook-loving doorknobs just like any other population of college students.

Ah, you seek refuge. This is as good a place as any, I suppose.

Re:My question: (1)

Samantha Wright (1324923) | more than 2 years ago | (#37925298)

Exhaustion is not quite true—every time a NASA article pops up, we get lavish replies from actual aeronautics engineers. I've also spotted a few other biologists ambling around; you can pick them out fairly easily because they don't seem to know how to speak in the active voice and say things like "is associated with" or "interacts with" instead of more specific verbal clauses. (That being said, they probably have real-world social lives.)

Maybe 2 Weeks (1)

eugene ts wong (231154) | more than 2 years ago | (#37923780)

Hi Samantha.

I think that they last about 2 weeks before being archived.

Re:Maybe 2 Weeks (1)

Samantha Wright (1324923) | more than 2 years ago | (#37924428)

I'll keep that in mind for the future.

How Many Germs Are Required To Get Sick? (1)

eugene ts wong (231154) | more than 2 years ago | (#37923850)

I was under the impression that just 1 is enough, but I figure that a single germ would have to overcome so many hurdles.

A quick Yahoo! search seems to indicate that there are a couple of theories for why we get sick. I ask because I don't want to become a germaphobe, and I do want to take it seriously.

Re:How Many Germs Are Required To Get Sick? (1)

Samantha Wright (1324923) | more than 2 years ago | (#37924536)

Everything—everything—in biology is a game of chance. The human body is extremely resilient to disease and uses a myriad of methods to protect against invaders in general, so it's very improbable that a human in a sterile room with a single bacterium or virion scattered somewhere in that room would show any symptoms. That being said, there are most certainly some diseases that can evade detection and overpower the immune system if they're able to get into the bloodstream via an exposed wound, even with as few as one or two particles. These are generally very serious diseases that you probably already know about: HIV, polio, and malaria, to name a few.

Re:How Many Germs Are Required To Get Sick? (1)

eugene ts wong (231154) | more than 2 years ago | (#37925284)

Thanks! That already clears up my perspective a bit.

1) Throughout life, I've been taught that drinking fluids can help to combat illness. I believe that fluids will boost the body's ability to manufacture things that combat germs, but does the body flush out germs using fluids? For example, if I have a germ on my hand, and the momentum of the tap water pushes it off, then the water physically removes it. It does not send white blood cells, and it does not use body heat to kill the germ. Does the body do something like that? If so, then how does it work? Does the germ get pushed through the rectum lining?

I hate to bombard you with so much, but I've often wondered.

Re:How Many Germs Are Required To Get Sick? (1)

Samantha Wright (1324923) | more than 2 years ago | (#37925442)

Drinking water doesn't directly have an effect on the body's ability to perform anabolic (constructive) chemical reactions. However, a dehydrated body is generally weaker than a hydrated one, because it limits our ability to expel unwanted chemicals through the urine. This means that our cells have to work harder to pump these chemicals out, constantly. Cells are like leaky boats that stay afloat because they constantly pump out unwanted molecules. When sick however, we excrete a lot of water, especially through sweating as a result of fever.

The body's only method for removing unwanted substances from the bloodstream is through the kidneys, which filter blood and leave undesirable elements, such as excess salt, in the urine. Some small viral particles most likely leave the body this way, however larger particles must be attacked by macrophages (white blood cells) or other immune cells first, and broken down into smaller components.

Re:How Many Germs Are Required To Get Sick? (1)

eugene ts wong (231154) | more than 2 years ago | (#37956770)

Great answer! You mentioned a lot of keywords that should be able to help me search for more information, if I am curious. I appreciate you offering your time.

2) Is there a way to help our bodies store excess water?

Re:How Many Germs Are Required To Get Sick? (0)

Samantha Wright (1324923) | more than 2 years ago | (#37959230)

Water with a little bit of sugar and salt is more effective at rehydrating the body than just straight water. Hence, the abominations that are sports drinks.

Re:How Many Germs Are Required To Get Sick? (1)

eugene ts wong (231154) | more than 2 years ago | (#37956834)

3) Let's assume that we got rid of those serious diseases which only need an exposed wound and 1 virus or bacteria. I'm curious about how easy it is to pass the remaining germs around if no hands are washed. I think that our hands are like rubber stamps, in that after several touches, we should pass less and less germs per touch. I'm really a wash-your-hands type of person, but I'd like to know if there is a guiding principle to knowing what's on my hand.

3.a) Let's say that somebody with a flu and a cold, coughs in his hand. If he handles 10 different things, then would you consider his hand to still be gross?

3.b) If I only wipe my hands on a dry paper napkin, and don't wash, after playing baseball, then what are the odds that I'll get germs in my mouth, while holding and eating a hamburger?

3.c) Will rinsing my hands with aggressive hand rubbing get rid of a significant amount of germs after that baseball game?

3.d) I live with people, who, after washing hands and before handling food, typically wipe their hands on their comfortable clothes that they wear around the home. It baffles my mind. How dirty are their hands?

Re:How Many Germs Are Required To Get Sick? (0)

Samantha Wright (1324923) | more than 2 years ago | (#37959316)

3. Unless you rinse with an ultraviolet bath or rubbing alcohol, there will always be some bacteria on your hands. It's not a bad thing; they are actually beneficial to have around. Washing your hands with water eliminates about 90% of the stuff on your hands, and soap is slightly more effective.

3. a. Yes, but like with all things related to biology, it doesn't matter as much as most people believe.

3. b. Pretty high—but your mouth is full of bacteria anyway.

3. c. See above. Water is pretty effective at cleaning hands.

3. d. As dirty as everything else around them.

Starting bioinformatics programming... (1)

thirdender (1412803) | more than 2 years ago | (#37950660)

Hi, This is a question I've been meaning to ask someone "in the know" for a while. I've been programming for years, but I never finished my CS degree. The last 3-4 years I've been doing website development full time, but I'm looking to... I'm looking to branch into new challenges. Biology has always fascinated me, but... I'm a cheap and lazy bastard who doesn't want to go back to school. Given those criteria :-p Do you think there is a need or place for someone willing to learn bioinformatics programming to help out with research? I have a fairly solid grasp of SQL, Unix principles, and I learn languages pretty fast. Is there a need for programmers who want to get in on almost a "wash beakers just to learn" kind of level, and if so could you recommend someone for me to contact? Thanks! Rob

Re:Starting bioinformatics programming... (0)

Samantha Wright (1324923) | more than 2 years ago | (#37956234)

One of the pervasive issues in the "wet lab" sciences (biology, medicine and chemistry) is that they're extremely steeped in meritocracy at the higher levels. Your worth is assessed, generally, by the number of acronyms after your name, or more importantly, by how many papers you've published and how much impact they've had.

Bioinformatics is a little better than this, because the field in its modern form owes a great debt to perl programmers and has a very open source attitude. Unfortunately, what demand for accreditation it eschews is replaced with a huge theoretical overhead. Even the basic introductory textbook I had in third year stood on top of five others, in linear algebra, statistics, genetics, cell biology, and comparatively advanced algorithmic techniques like dynamic programming. In order to contribute meaningfully to the field, a formal learning environment is pretty much unavoidable.

Re:Starting bioinformatics programming... (1)

thirdender (1412803) | more than 2 years ago | (#37966148)

Got it :-p Thanks, I was kind of worried about that. Was still curious though :-)

Thanks for your answer!

Concerns About Things Other Than Germs (1)

eugene ts wong (231154) | more than 2 years ago | (#37956880)

4) You have probably heard of the idea that eating a few germs gives our immune system something to do, which strengthens it. Therefore eating something that might have fallen on the floor, or touching something dirty before returning to food handling, are all okay. I believe that there is significant truth to that, but I also believe that people are not thinking about it thoroughly. I think that we have to be concerned about more than germs. Are there chemicals or substances that we might need to be concerned about?

Thanks again!

Re:Concerns About Things Other Than Germs (1)

Samantha Wright (1324923) | more than 2 years ago | (#37960050)

Well, cleaning products tend to be fairly unpleasant—but in general, unless you're drinking bleach, their contribution to poor health is essentially negligible. If you keep your body fortified with vitamins and other essential-but-minor nutrients, you have little or nothing to worry about.

Re:Concerns About Things Other Than Germs (0)

eugene ts wong (231154) | more than 2 years ago | (#37963790)

Great! Thanks for the answers.

It was funny to see you post at Score:0. I think that somebody doesn't like you and/or your answers. :^D

Re:Concerns About Things Other Than Germs (1)

Samantha Wright (1324923) | more than 2 years ago | (#37965632)

It definitely looks that way—perhaps thirdender wasn't too happy.

Re:Concerns About Things Other Than Germs (1)

eugene ts wong (231154) | more than 2 years ago | (#37970854)

I don't think that he can mod down, if he's unhappy, though, because he already posted in the discussion.

Re:Concerns About Things Other Than Germs (1)

Samantha Wright (1324923) | more than 2 years ago | (#37975040)

He was probably feeling fairly okay, given his reply—but still, there are plenty of people out there with puppet accounts.

Speciation (1)

rjh (40933) | more than 2 years ago | (#37967254)

What is the accepted definition of speciation, and have we ever directly observed a speciation? The obvious definitions I've found have all been lacking: e.g., "if they can produce viable offspring together, they are the same species" fails to account for ligons, tigers, polar/grizzly hybrids, and so forth.

Re:Speciation (1)

Samantha Wright (1324923) | more than 2 years ago | (#38001634)

I have mostly bad news for you: there's debate about what constitutes speciation [wikipedia.org] , and has been since the time of Darwin. However, the generally accepted definition is that two animals are of the same species if they bear significant genetic differences and naturally do not have a means of being reproductively viable (perhaps their gametes can fuse but their genitalia are incompatible, or perhaps they're physically isolated, etc.) although there are examples that violate even this. When two populations aren't sufficiently distinct genetically, but isolated in such a way that speciation is an inevitability, they are called incipient species. Still, what constitutes 'sufficiently distinct' is up for debate. As you will read in the above link, the concept of "species" is a human invention; in fact all levels on the taxonomic tree are pretty arbitrary, and exist primarily to help us classify and break down our world into more manageable chunks. Deep down, it's just a system of convenience.

There are quite a few examples of speciation events that are ongoing and have been noted by biologists. You can read about some of them over here [wikipedia.org] , which also discusses the different kinds of species separation processes that can occur. Speciation is potentially a very slow process, however, which can take hundreds of thousands, if not millions, of years. It would be a bit of a challenge for us to watch any of the events with broad appeal. :)

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