# Ask a Biologist



## Herp

pneumoceptor said:


> Here's my best answer!


Good answer!

I'm actually a pharmacy/biochem grad student, so you could have gotten a bit more chemical when it required to do so. My pet peeve with phytotherapics as they are being taken in my country is that they take a plant, let's say _Melissa officinalis_ and test for anxiolytic characteristics. The tests yield good results and soon, media is all over the place, claiming that M. officinalis is the BEST TREATMENT EVER for anxiety.

The thing is, while the labs are concerned with identifying potential candidates (And you are absolutely right on that we can't just go on and mass produce anything), what is eventually commercialized is dried extracts from the plant, where they get encapsulated and sold. It's cheap to do so and it sells due to the hype.

But I have seen countless examples of people that would take a phytotherapic over a synthesized drug even if their pharmacological effects are the same, often claiming that the extract is better because it's 'natural'. While I recognize that there are downsides to synthetic drugs, phytotherapics also represent a risk in that their content is not entirely controlled.

Other than that, any other point I had was well addressed in your video. 

Nice job!


----------



## nonnaci

pneumoceptor said:


> Insightful question (in that you kind of answered it yourself, which I realized about halfway through addressing it  )...


Thank you for the response. I figured the problem wasn't going to be like particle simulations commonly done in the physics community but rather a statistical model like using markov states. Such a state space must be quiet huge with multiple local energy minimums to warrant the use of a distributed approach. On a side tangent, there was another project (forgot the name) that turned part of this process into a game where users could "spot" low energy configurations as to give the models closer initial conditions to the optimal. Its computational crowdsourcing ftw.


----------



## pneumoceptor

Herp said:


> Good answer!
> 
> I'm actually a pharmacy/biochem grad student, so you could have gotten a bit more chemical when it required to do so. My pet peeve with phytotherapics as they are being taken in my country is that they take a plant, let's say _Melissa officinalis_ and test for anxiolytic characteristics. The tests yield good results and soon, media is all over the place, claiming that M. officinalis is the BEST TREATMENT EVER for anxiety.
> 
> The thing is, while the labs are concerned with identifying potential candidates (And you are absolutely right on that we can't just go on and mass produce anything), what is eventually commercialized is dried extracts from the plant, where they get encapsulated and sold. It's cheap to do so and it sells due to the hype.
> 
> But I have seen countless examples of people that would take a phytotherapic over a synthesized drug even if their pharmacological effects are the same, often claiming that the extract is better because it's 'natural'. While I recognize that there are downsides to synthetic drugs, phytotherapics also represent a risk in that their content is not entirely controlled.
> 
> Other than that, any other point I had was well addressed in your video.
> 
> Nice job!


Yeah, I guess I didn't really get the nuance that we're talking about more "herbal" medicines than clinical trial-proven, mass produced medicines. Again, I'd say that whatever works works. But anything that doesn't have statistically significant results above placebo in double blind tests doesn't work, in my opinion . Where do you live, out of curiosity?


----------



## pneumoceptor

nonnaci said:


> Thank you for the response. I figured the problem wasn't going to be like particle simulations commonly done in the physics community but rather a statistical model like using markov states. Such a state space must be quiet huge with multiple local energy minimums to warrant the use of a distributed approach. On a side tangent, there was another project (forgot the name) that turned part of this process into a game where users could "spot" low energy configurations as to give the models closer initial conditions to the optimal. Its computational crowdsourcing ftw.


Yes, statistical models seem to be the way to go, but they're still exceedingly simple compared to what's actually going on. And yes, proteins fold along energy landscapes that can be smooth or rugged or have clear low energy native states, and each protein has a different folding landscape with different energy minima representing different three dimensional ensembles. It's all quite complex. Add to it macromolecular crowding, and I don't know how we'd even begin to model it adequately.

Here's an image representing the environment within a bacterial cell:









And mammalian cells are orders of magnitude more complex than this.

And to add some NF perspective to it, isn't life beautiful and complex and amazing?!


----------



## nonnaci

pneumoceptor said:


> And to add some NF perspective to it, isn't life beautiful and complex and amazing?!


And self-organizing :laughing:


----------



## Adrift

"In a paper published in the July 11 online issue of Science Translational Medicine, researchers at the University of California, San Diego School of Medicine have identified two key regulatory proteins critical to clearing away misfolded proteins that accumulate and cause the progressive, deadly neurodegeneration of Huntington's disease (HD)."
LINK

I don't know if this is your group, but congrats if it is. Hope you don't mind the derail. I'm sure I'll have questions after I read the paper.


----------



## Anonynony

Let's say you got a pretty gnarly cut on your leg. Now let's say you got a pretty gnarly cut on your other leg. The two cuts fit perfectly together. You stick your cuts together & bandage them up. 
Would your legs fuse together?(I'm assuming yes)
& B, how long would it take?


----------



## Anonynony

pneumoceptor said:


> Yes, statistical models seem to be the way to go, but they're still exceedingly simple compared to what's actually going on. And yes, proteins fold along energy landscapes that can be smooth or rugged or have clear low energy native states, and each protein has a different folding landscape with different energy minima representing different three dimensional ensembles. It's all quite complex. Add to it macromolecular crowding, and I don't know how we'd even begin to model it adequately.
> 
> Here's an image representing the environment within a bacterial cell:
> 
> View attachment 42565
> 
> 
> And mammalian cells are orders of magnitude more complex than this.
> 
> And to add some NF perspective to it, isn't life beautiful and complex and amazing?!


Ooh! Pretty! I might have to paint that!


----------



## Herp

pneumoceptor said:


> Yeah, I guess I didn't really get the nuance that we're talking about more "herbal" medicines than clinical trial-proven, mass produced medicines. Again, I'd say that whatever works works. But anything that doesn't have statistically significant results above placebo in double blind tests doesn't work, in my opinion . Where do you live, out of curiosity?


I live in the country that is home to the amazing Amazon Rainforest, Brazil. Science here still is on its baby steps, but it's something fun to participate in nevertheless.


----------



## pneumoceptor

Herp said:


> I live in the country that is home to the amazing Amazon Rainforest, Brazil. Science here still is on its baby steps, but it's something fun to participate in nevertheless.


I work with a couple of Brazilian postdocs. They've told me about how your country is pouring money into scientific research. That's wonderful!


----------



## pneumoceptor

FigureSkater said:


> Let's say you got a pretty gnarly cut on your leg. Now let's say you got a pretty gnarly cut on your other leg. The two cuts fit perfectly together. You stick your cuts together & bandage them up.
> Would your legs fuse together?(I'm assuming yes)
> & B, how long would it take?


Hahaha, that's a fun question. Yeah, my guess is that they would fuse together, but stitching might be necessary to keep the different epidermal/dermal/etc layers at the right orientation. How long would it take... I don't know . Are you planning on running an experiment?


----------



## pneumoceptor

Adrift said:


> "In a paper published in the July 11 online issue of Science Translational Medicine, researchers at the University of California, San Diego School of Medicine have identified two key regulatory proteins critical to clearing away misfolded proteins that accumulate and cause the progressive, deadly neurodegeneration of Huntington's disease (HD)."
> LINK
> 
> I don't know if this is your group, but congrats if it is. Hope you don't mind the derail. I'm sure I'll have questions after I read the paper.


Interesting study. No, that's not my group, but it's definitely a study my group would be interested in. Thanks!


----------



## shampoo

why do we randomly get adrenaline rushes, even if we are in no danger or exciting situation, just sitting on the sofa...and randomly get an adrenaline rush!?

annnd do fish have feelings?


----------



## Anonynony

pneumoceptor said:


> Hahaha, that's a fun question. Yeah, my guess is that they would fuse together, but stitching might be necessary to keep the different epidermal/dermal/etc layers at the right orientation. How long would it take... I don't know . Are you planning on running an experiment?


Hmm....Nope!:tongue: But if someone did that they could be a mermaid lol


----------



## pneumoceptor

FigureSkater said:


> Hmm....Nope!:tongue: But if someone did that they could be a mermaid lol


Wow. After reading that, I thought to myself, this *must* be an Ne user. And then I verified this on your profile page .


----------



## Anonynony

pneumoceptor said:


> Wow. After reading that, I thought to myself, this *must* be an Ne user. And then I verified this on your profile page .


I literally laughed out loud when I read this :tongue:


----------



## Stelmaria

I have a question, though it doesn't have to be answered in a video.

The first generation monoclonal antibodies are coming off patent within the next few years and some of them have revenues in the hundreds of millions to billions of dollars per year. Obviously this is a ripe area for generic drugs. However monoclonal antibodies are produced using biotech methods rather than chemical synthesis, and apparently many of the generics being developed aren't actually the same thing, but merely 'biosimilar'.

My question is how 'similar' are 'biosimilar' drugs in the monoclonal antibody class and perhaps related drug classes (other biotech manufactured drugs)?

Lets say that recombinant technology was used to make a clone of the antibody in transgenic tobacco plants (apparently this is cheaper than cell culture), wouldn't this be considered identical (if complete and pure) and thus negate the need for additional clinical trials (for safety and efficacy)?


----------



## Luke

I have a very basic question  I have heard that the DNA double helix is connected by base pairs. What exactly are base pairs?


----------



## pneumoceptor

shampoo said:


> why do we randomly get adrenaline rushes, even if we are in no danger or exciting situation, just sitting on the sofa...and randomly get an adrenaline rush!?
> 
> annnd do fish have feelings?


Heya... I'm sorry I missed these questions before!

As far as adrenaline, I'm no endocrinologist... but I can say that the body is exceptionally complex, and there are all sorts of signalling cascades, with feedback loops within feedback loops. So there's so much playing into all of these processes that any number of factors can lead to responses like adrenaline rushes. Some of them can be conscious, some can be subconscious, some can be "hard-wired". 

As far as fishes' feelings... if you mean, can they feel pain (physically), absolutely. If you mean, can they be scared, absolutely. The more "primal" feelings that keep organisms from getting killed are present in fish. If you mean, can they feel sad... the more complex emotions... who knows?! It would be difficult to do an experiment that could give a definitive answer there. What do you think?


----------



## pneumoceptor

@Snow Leopard, here's my answer to your therapeutic antibody question:


----------



## pneumoceptor

pumpkins said:


> I read this somewhere..: Is it true that since our body regenerates cells all the time, that after a certain amount of years we will be completely "new" - that none of the cells from 10/30/how many? years ago are there anymore and that not a single part of our then-body exists anymore?
> Sorry for the lack for scientific terms, I don't know how to use them.


Neat question .


----------



## pneumoceptor

bigtex1989 said:


> When you drink hot beverages, how does your body maintain your proper body temperature?
> 
> I know that when drinking cold water (less than 37 degrees C) your body must use energy to raise the temperature of the water before it can be used. What is the analog for hot water? Does your body have to wait for the liquid to cool before use?


It's neat to see your gears turning . Great question.


----------



## pneumoceptor

Remcy said:


> If man was to live in zero gravity (i.e space), how would evolution shape the human physiology?


This is definitely a question for an Ne user! Anyone else want to tackle it too?


----------



## pneumoceptor

Hudson said:


> I've read a little about artificially created organisms. i am not a biologist, nor am I particularly educated about it beyond a high school level. But I was wondering if it would be possible to create an organism designed to thrive in any particular situation. I mean, obviously there are places where this would be impossible, like an environment made out of things destructive to DNA, or something like that.
> 
> But how far can we go? What's the most extreme environment we could make an organism thrive within? Could we make it so that it produces a particular by product, other than methane, oxygen, or CO2?
> 
> Thanks.


Very relevant, interesting question!


----------



## bigtex1989

Remcy said:


> If man was to live in zero gravity (i.e space), how would evolution shape the human physiology?


Since an idea person was invited to take a swing at this, I guess I'll go ahead XD

To start, a clarification must be made. Do humans of today just move to space in space ships without artificial gravity? Did the single cells we came from just start in space? Does this zero g environment have resources such as water and air? Or is it like space? I need more specifics! 

Without that, I'll give some different scenarios and state the assumptions made.

1. The least interesting case is probably humans of today move in to space. @pneumoceptor already gave a pretty good explanation, but I would venture to say it would be even less noticeable. The mechanisms for evolution are time and death and preferential selection. I think as "sentient" species, we have moved a bit past preferential selection. Eventually, I think those with the strongest hearts (and entire circulatory system by extension) would survive the longest and mate the most leaving humans with better cardio. That's about it XD. Also smelling might evolve to become more potent. Which might mean pheromones would eventually become way more powerful....this has a lot of fascination implications! For example, a group of humans moves into space. They develop better olfactory systems AND increased pheromone production (to counter the affects of space on smelling). Then they move back to Earth. They would be the most desired mates and thus this mutation lives on!

2. Cells evolved on planets with negligible gravity....for resources XD. For this, let's assume that cells can clump together and don't just bounce off when they touch lol. Starting from the inside out, our bone structure is probably most heavily influenced by gravity. Since our bones wouldn't have to withstand any sort of stress, I imagine the bones would start out paper thin or be non-existent. Depending on how violent this new species is would really tell how dense bones would be. I also imagine in zero g, the dominant species would be able to change their own density at will. Kind of like how we can do SLIGHTLY by sucking in a bunch of air and floating on water, but they would be able to do it to a much greater extent. They probably wouldn't have feet. Why would you need them? More complex and less clumsy hands would probably be advantageous since if you touch something, it would just bounce off. A propulsion system would need to develop. Since there are particles around, the most likely scenario would be to develop some sort of tail to hit them and move you forward. Since body structure is clearly different, the circulatory system would be too. As before, it would need to be stronger. Veins would probably be smaller to create pressure differences more easily. The body would evolve to need less oxygen, seeing as how it would be much harder to get some since circulation of air would be limited. This means "humans" would probably be smaller than they are today. Competition for resources tends to bring about smaller overall species but more variation in size. This implies that mates would be selected for size which means a tournament species. The psychology of the species might be way more violent because of the scarcity. Twins would be almost unheard of, the larger gender would not care for the young, society kind of like apes. As for facial structure, I don't see why any sensor would be different (barring the differences in the nervous system). Skin would be much thinner since it would be infinitely hard to be cut by your environment, however, this also has to do with solar radiation. So all things equal, the skin (or membrane) would be much thinner. I started this wanting a comprehensive guide, but I'm starting to get bored now. In short, I imaged humans to look more like mermaids with better hands. Although this is probably inaccurate and inconsistent with my description above!


----------



## Hudson

pneumoceptor said:


> Very relevant, interesting question!


I was basically talking about bio remediation and, since Im a geek, terraforming.  You clarified a bunch of things I was wondering about. 

No, thank you! SCIENCE! ^_^

Appreciate you taking the time.


----------



## pneumoceptor

Hudson said:


> I was basically talking about bio remediation and, since Im a geek, terraforming.  You clarified a bunch of things I was wondering about.
> 
> No, thank you! SCIENCE! ^_^
> 
> Appreciate you taking the time.


Yeah, bioremediation is a great application of synthetic biology. I'm actually looking to land a job with a green energy company to engineer fungi to produce enzymes that make plant products more accessible as fuel. It's not dealing with pollution per se, but it's a similar line of thought.

Re: terraforming... I just looked up your profile... yup, Ne .


----------



## Hudson

pneumoceptor said:


> Yeah, bioremediation is a great application of synthetic biology. I'm actually looking to land a job with a green energy company to engineer fungi to produce enzymes that make plant products more accessible as fuel. It's not dealing with pollution per se, but it's a similar line of thought.
> 
> Re: terraforming... I just looked up your profile... yup, Ne .


Cool! Yeah, Im a baby-fresh graduate of earth science 101. Don't know what I'm going to do yet, but that class touched on many things I think I would be happy doing. I like knowing how things work. And yes, speculating too. ^_^ After your response, I couldn't help but think of moores law as it applies to the genome. We live in an exciting time.

I should graduate just in time to be in the thick of things.

It would be great to start getting those environment-friendly applications going. Good luck with that job.

Only Ne think about terraforming?  I must confess I read plenty of science fiction.


----------



## mrgreendots

I just remembered another thing I've been wondering about.
Why does the area around your diaphragm ache when you're depressed?


----------



## Stelmaria

I know one of your previous videos discussed extremophiles, I was wondering what were your favourite extremophiles? I am particularly curious about microbes that have evolved to thrive in man-made conditions, such as nuclear reactors and in space/low gravity conditions.

It still seems amazing that a small tolerance for heat and dryness for example is all that is needed for a very small proportion to survive and this process leads to selection over countless generations to lead to a fully fledged "new" species of bacteria.

I guess this is similar to the process by which the adaptive immune system can adapt extreme affinity for any molecular target, starting with extremely poor affinity and refining over many generations of somatic mutations combined with a selection process.


----------



## JYFly

Didn't see anything related to death when I searched the thread, so apologies if this has already been asked.

I have heard two reasons so far as to why we die of old age: 1) telomeres shortening as a cell divides, and 2) DNA damage over time resulting in the organism not working as efficiently. I've also heard that because of the frequency of DNA damage, anyone would end up getting cancer if they lived long enough.

It's obviously easier said than done, so do you agree or disagree that theoretically, an organism would have an indefinite life span if one or both of these were prevented?


----------



## hulia

Aw this thread is so cool. I wish it still remained active. Sorry for the bump! As a microbiologist in training myself, I greatly enjoyed flipping through all 14 pages.


----------



## FlightsOfFancy

Do you think Deep Brain Stimulation will ever be used for more disorders than OCD?

How exactly does that work?

Do you believe in psychotropic medication?


----------



## pneumoceptor

mrgreendots said:


> I just remembered another thing I've been wondering about.
> Why does the area around your diaphragm ache when you're depressed?


I have no idea! I haven't experienced this, I don't think. Have you found many others who have also experienced this?


----------



## pneumoceptor

Snow Leopard said:


> I know one of your previous videos discussed extremophiles, I was wondering what were your favourite extremophiles? I am particularly curious about microbes that have evolved to thrive in man-made conditions, such as nuclear reactors and in space/low gravity conditions.
> 
> It still seems amazing that a small tolerance for heat and dryness for example is all that is needed for a very small proportion to survive and this process leads to selection over countless generations to lead to a fully fledged "new" species of bacteria.
> 
> I guess this is similar to the process by which the adaptive immune system can adapt extreme affinity for any molecular target, starting with extremely poor affinity and refining over many generations of somatic mutations combined with a selection process.


I think the nuclear extremophiles you mentioned are quite amazing. What are your favorites?

Yes, only a tiny selective advantage is all that's needed to begin to separate out subpopulations. Sometimes there's no way to amplify the advantage, but sometimes there is. And yes, that's a great analogy to the adaptive immune system. There, again, like you mentioned, there's genetic variability that can be inherited. Biology is amazing .


----------



## pneumoceptor

FlightsOfFancy said:


> Do you think Deep Brain Stimulation will ever be used for more disorders than OCD?
> 
> How exactly does that work?
> 
> Do you believe in psychotropic medication?


I'm sorry to say that I know nothing about deep brain stimulation other than what wikipedia just told me! Just from that article, what I can take from it is that it sometimes works, and in a statistically significant manner, but that we don't know why it works. What are your thoughts?

Regarding your psychotropic medication question, I'm not sure what you mean, do I 'believe' in it... I mean, there are ways in which it's proven to increase quality of life, right? If you mean, do the benefits outweigh the cost, I think that can only be decided by the person considering it. What do you think?


----------



## pneumoceptor

JYFly said:


> Didn't see anything related to death when I searched the thread, so apologies if this has already been asked.
> 
> I have heard two reasons so far as to why we die of old age: 1) telomeres shortening as a cell divides, and 2) DNA damage over time resulting in the organism not working as efficiently. I've also heard that because of the frequency of DNA damage, anyone would end up getting cancer if they lived long enough.
> 
> It's obviously easier said than done, so do you agree or disagree that theoretically, an organism would have an indefinite life span if one or both of these were prevented?


Thanks for the question!


----------



## mrgreendots

pneumoceptor said:


> I have no idea! I haven't experienced this, I don't think. Have you found many others who have also experienced this?


I haven't asked my friends about it but when i tried to research it there were quite a few people with the same question so I guess others have too. Might it have something with Sympathetic nervous system being accelerated due to stress?


----------



## pneumoceptor

mrgreendots said:


> I haven't asked my friends about it but when i tried to research it there were quite a few people with the same question so I guess others have too. Might it have something with Sympathetic nervous system being accelerated due to stress?


It could be... there are many many reasons why this might be the case. The fact that it's not apparent in scientific literature why it is leads me to believe that it's a complicated reason or set of reasons.


----------



## Adrift

Are roaches of any use to humanity? Yes, they eat stuff and help break down human garbage, but we do have landfills and incinerators. Would humanity miss the roach if it became extinct?


----------

