text:
How long does an Audiomoth acoustic logger record for?
I'm wanting to record bat echolocation calls using an Audiomoth recorder. However, I can't find out anywhere how long these recorders can record for on a full charge.
What is the longest duration someone has deployed these recorders for, for the purposes of recording bat echolocation, and at what duty cycle (recording continuously, or just at dusk for a few hours?)
Additional info in the comments:
They operate using 3 AA batteries.

Audiomoth is apparently the designation of the circuit module, could you tell us what power-supply you're using?

They operate on AA batteries (3x)...

AA batteries vary in capacity by a factor of more than 6 times (Wikipedia). This is a tricky on-off-topic question, because we need to establish things which are more suited to our [electronics.se] stack. I'll try anyhow. With the most powerful batteries, the tech spec sheet indicates you should get just a shade under 3 days/nights continuous use - but the device can be programmed to go into sleep-mode making it maybe 6 nights in total. Can you code?

when recording high sample rate and continuously through the night (e.g. around 8hrs), then they will last about 3 nights or so.  If you sample discontinuously then you will obviously get a longer deployment time. The new firmware also provides a triggering mechanism that will allow much longer deployment times - see here:
https://www.openacousticdevices.info/support/announcements/audiomoth-configuration-app-1-7-0-firmware-1-8-0
Also - useful advice on Audiomoths generally is available at Tessa Rhinehart's GitHub (https://github.com/rhine3/audiomoth-guide) and at Wildlabs.net.

I use Audiomoths for recording bats. If you are looking for continuous recording, depending on your sample rate (you want your sample rate to be at least twice the highest frequency you expect to record--256kHz should be good if you are in the US/Europe) you should be able to get 3 nights. The key here is the word "should." I've had batteries and Audiomoths do weird things in the field, so if the data are critical, I strongly recommend having redundancy if that's an option, meaning two Audiomoths recording at the same time. I also recommend changing the batteries at least one day earlier than when you think they should last until.
Another thing related to your question: consider where you place your Audiomoth and if a curious squirrel/raccoon/deer might chomp on it and affect your recording duration. Speaking from experience, I highly recommend the hard case.

You can also add an external battery pack with a little soldering which can make the devices last much longer. e.g. https://twitter.com/freaklabs/status/1529915274853502980

@macster110 You beat me to it - was about to post the same +1

With an earlier version of the Audiomoth (v 1.1.0), I had continuously recorded at 384 kHz with duracell rechargable batteries, followed by another round with duracell ultra batteries. The latter lasted the longest for around 2.5 days. So it fluctuates based on the types of batteries recommended and some commercial rechargable batteries usually have a faster drain life.
More recently, Akiba from Freak Labs (https://twitter.com/freaklabs/status/1529915274853502980) has been experimenting with extending battery life using an external battery pack. So this could be a possible solution if suitable.


text:
Is it true that pigeons became less afraid of humans in recent years?
My grandfather had told me when I was a kid that at his time the pigeons would not approach humans closer than about 15 meters. At the time he said it the pigeons were approaching us not closer than approximately 1.5-2 meters. And now I often have to make efforts so not to step on a pigeon who hinders my movement along a street.
This is in Europe.

I think it is possible that populations can change their behaviour rather fast, but "Europe" is too big to make a statement about. For example I did an image search for "city pigeon 1950s" and got pictures like this one: https://s-media-cache-ak0.pinimg.com/736x/3a/38/34/3a383400d1749e7b1019bc90bdcb43f1.jpg

source: Stack Exchange

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text:
Why mushrooms have so much antibiotics?
Why they have much more antibiotics than plants for instance?

The discovery of natural antibiotics seems to have been most successful in molds like the fungal species  Penicillium chrysogenum and the bacterial species Brevibacillus brevis. As @notstoreboughtdirt points out, plants have their own mechanisms. It's not quite clear what you want to know since a complete answer could be a thesis.

This isn't fully understood but one theory is that they live in soil feeding off dead things and so are in competition with bacteria and other fungi for resources including space.  The antibiotic compounds they produce have been described as a sword and shield.  Some compounds are offensive (sword) and attack other fungi and bacteria while other compounds protect a species (shield) from the compounds of other organisms seeking to do the same thing to them.  This is only half the story really, fungi also excrete compounds that look similar to antibiotics but have no known function.  Still other compounds have seemingly no effect on other organisms but when taken by humans and other mammals lower cholesterol in the blood. Strange thing for a fungus to produce.

Hi and welcome to Bio.SE. Whilst the question itself is likely to be closed, but generally, answers here should be well cited. Personally, I'd be interested to find out more about the additional excreted compounds.

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text:
Effect of UV radiation on retinoid (vitamin A) receptors in the skin
The retinoid receptors in the skin (face) can be disabled by UVA sun radiation as these study states : https://www.sciencedaily.com/releases/1999/03/990331063314.htm
In this article it says the same : http://www.abc.net.au/news/science/2015-11-18/how-uv-light-damages-our-skin/6856742

" UVA activates receptors that produce the enemy of firm skin: matrix metalloproteinases. These enzymes have one job and they do it beautifully: breaking down collagen. And it doesn’t take much UV at all to get this going, so even without sunburn any parts of your skin that are exposed to the sun will age.

As if the collagen attack wasn't insult enough, UV radiation also interferes with the production of Vitamin A receptors on our skin cells.
Vitamin A is critical for cell growth in our skin, but without functioning receptors for the vitamin to activate, our skin ends up thinning, and that’s something no amount of carrots can fix.
Question is: do these receptors actually work again after sun exposure is stopped? Or any topical/oral treatment with vitamin a will be useless for skin regeneration?
Thank you

Please do not write titles like this again. It appears as a shameless attempt to draw attention to your question. I have given it a minimal edit rather than voting for it to be removed. Please take note.

@David The title stood to be improved, but the original doesn't appear to be at all untoward like you've indicated... certainly not "a shameless attempt to draw attention". Maybe just silently improve it next time instead of admonishing a new user unnecessarily.


text:
Why do retroviruses go through a DNA stage to replicate their RNA genome?
Why do retroviruses (e.g.HIV) convert their RNA genome to DNA (using reverse transcriptase) and then transcribe it back into viral RNA (and translate that into viral proteins). Surely to replicate their genome it would be simpler to use RNA-dependent RNA polymerases as RNA viruses like Measles Virus do.

Biology isn't as stringent as quantum physics, but still, "everything which is not forbidden is allowed." Retroviruses use reverse transcriptase because a) they can and b) it works. You can get into complex evolutionary arguments about comparative benefits, but ultimately retroviruses stick around because reverse transcriptase works well enough for them to continue to survive. Evolution isn't goal oriented - it doesn't seek simplicity just for simplicity's sake. What works, works, and what doesn't, doesn't.

I now feel my previous comments were based on a misunderstanding of the question. On this basis I have withdrawn them, answered the question, and reversed my close vote. The question is still very basic, but I can see how you might have become confused if the subject was not introduced to you properly.

I have changed your title and question to clarify  it as several people have been confused by it. If this is not what you meant could you please elaborate.

I am going to focus the answer on mainly "why HIV virus has evolved such mechanisms to go from RNA to DNA and back to RNA when it could simply use the first RNA to make its copies". While others have already discussed the broad point, I will discuss more about the details. There are a few points which might support this, all of which basically come down to evolution.

Increased Mutations: the process of conversion of viral RNA to DNA is carried out by the viral enzyme reverse transcriptase. The point here is that this process of reverse transcription is extremely error prone (Zheng et al, 2005), which increase its chances of evolving drug resistance and other abilities.
Recombination: again, the enzyme reverse transcriptase possesses ability to cause recombination of viral DNA. During recombination, the nascent DNA can switch multiple times between the two copies of the viral RNA (Charpentier et al, 2006), known as copy-choice recombination, and can rapidly shuffle the genetic information between the parental and progeny genomes.
Post-transcriptional modifications: after the viral DNA is completely transcribed, it undergoes splicing to form mature mRNA. These mRNAs lead to production of viral proteins Tat and Rev. Accumulationof Rev inside nucleus allowes the full mRNAs to leave the nucleus and form viral genomes or structural proteins Gag and Env (Pollard et al, 1998). Thus, reverse transcription is vital for the virus.

References:

Zheng YH, Lovsin N, Peterlin BM (2005). "Newly identified host factors modulate HIV replication". Immunol. Lett. 97 (2): 225–34.
Charpentier C, Nora T, Tenaillon O, Clavel F, Hance AJ (2006). "Extensive recombination among human immunodeficiency virus type 1 quasispecies makes an important contribution to viral diversity in individual patients". J. Virol. 80 (5): 2472–82.
Pollard VW, Malim MH (1998). "The HIV-1 Rev protein". Annu. Rev. Microbiol. 52: 491–532.

"extremely error prone (Zheng et al, 2005), which increase its chances..." - Do viruses - retroviruses -  have anything better, any proofreading at all? (cp. "what works, works")

I'll assume that "better" here means "better than other RNA viruses". In that case, I don't think so (I haven't looked into it, but coming from the observation that a lack of proofreading is somewhat beneficial for the virus, I think it's safe to deduce that the retroviruses would stay away from things like proofreading. Also, I doubt there would be quantitative studies regarding comparative analysis of proofreading activities of retroviruses and other RNA viruses).

Much later, from DNA back to RNA, there's none, I guess. Thanks!

Interpreting the question
Initially I interpreted the question as little more than “Why one type of virus rather than another?” (dsDNA. ssDNA, ssRNA [+ve v. –ve] etc.), and this (which would be unanswerable) was the way @Taimur seems to have understood it. And I also felt that the poster’s reference to ‘complexity’ reflected more his familiarity with other viruses than any real appreciation of what is complex in a molecular manner.
However I now think I misunderstood the question because of not appreciating the erroneous assumption on which I believe it is based. If I am correct, it could be rephrased in the following manner to make that assumption clear:

“If the only purpose of integrating a DNA copy of the retroviral RNA
  into the host genome is to replicate the RNA in the virion, why is an
  RNA-dependent RNA polymerase not used as in other RNA viruses?"

Answer

This stage of the retroviral life cycle in which a DNA copy is
  integrated into the host genome is not an incidental stage in a
  mechanism to replicate the virion RNA — it is the key element of the
  modus operandi or strategy of existence of the virus.

Explanation
As explained in the first paragraph of the Wikipedia article on retroviruses, once integrated into the host genome it can persist there:

“The host cell then treats the viral DNA as part of its own genome,
  translating and transcribing the viral genes along with the cell's own
  genes…”

One way of thinking of this is as a strategy the virus adopts for ‘hiding’ until circumstances are suitable for it to produce more infectious progeny. One might even regard the form that is integrated into the host DNA as the viral genome — rather than the form that is encapsulated by lipid and protein into virus particles.
This sort of lifestyle is similar in some ways to that of certain DNA bacteriophages that can produce either lytic or lysogenic infections. Such persistence of viral genomes in the host is also seen in some eukaryotic DNA viruses like herpes simplex virus, in which an individual may have what is called a latent infection, which produces occurrences of cold sores (in the case of HSV1) throughout the lifetime of the individual as the virus is activated from time to time by various stimuli.

Is there some intermediate stage before the "DNA stage" where the virus is being translated from its RNA for presentation on MHC? Or, do cells have to wait, always? E.g. HIV Immune Evasion: Disruption of antigen presentation...Elizabeth R. Wonderlich et al. ("Perseverance is no evasion")

There is an excellent freely available account of reverse transciption here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3475395/pdf/cshperspectmed-HIV-a006882.pdf. From which you will see (Fig 1)that reverse transcription takes place on the viral RNA. I don't know whether there is sufficient enzyme in the virion to catalyse this — I imagine some translation has to occur, but this is not for providing a template for reverse transcription. I don't know what relevance presentation for MHC has to this, and in any case it is not an area I know anything about.

Viruses are one of the particles whose evolutionary origin is still a mystery to scientists. Various hypotheses have been presented but none of them have been proven so far.
However, as one of our commenters has said, "What works, works and what doesn't, doesn't." This is the basic concept of the evolutionary theory. All organisms which can survive in an environment using a certain adaptation, whether it takes more time or less time, will survive and continue using the same adaptation.
One more point to consider is that individual organisms never evolve, only populations (organisms of the same species living in the same area at the same time) evolve. This means that a retro virus will not change to adapt to a simpler method just because it takes less time. If conditions arise that do not favour retroviral method of using reverse transcriptase but favours the method of other RNA viruses, then retroviruses will simply then decrease in number until they are zero and RNA viruses will survive.
I hope to have satisfactorily answered your inquiry.

Well, dude! You are not writing a letter. While we do expect formal language in questions and answers here, please don't post "overformal" answers.

@another'Homosapien' I will make sure to avoid that next time. Thank you.

@another'Homosapien' I have made the edits.

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What happens if the Nematode epidermis becomes damaged?
This animal has a hydrostatic skeleton which lets it move. If we damage the epidermis and fluids come out, can the nematode still move ?

Nematodes have external skeleton in the form of a cuticle. Their muscles are attached to this external skeleton and when a muscle cell contracts it moves a segment of the cuticle relatively to the other segments, which in turn allows the pushing of the environment and thus, motility. This is very similar to how we, humans, move.
Damaging the cuticle in nematodes results in motility impairment. For example, some C. elegans strains have a mutation that results in a non-normal cuticle formation which makes the animals roll instead of moving peristaltically (like a snake).
In addition, some muscles are not skeletal muscles, or body wall muscles in the case of nematodes. These muscles affect movement of an organ like the pharynx in nematodes or the heart in humans.
for further reading regarding the body wall muscles and cuticle interaction you can see wormatlas.org
References:

Labouesse, M. 2006. Epithelial junctions and attachments. WormBook, ed. The C. elegans Research Community, WormBook, doi/10.1895/wormbook.1.56.1

Please add some references to your answer.

What type of reference is expected in this site?

peer-reviewed, possibly from a well known journal or site, cited by many others...in short, authentic.


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How is NAD+ used in lactic acid fermentation after it is oxidized from NADH?
I am confused with the whole process of glycolysis and the fate of the products of this reaction. So, I understand that anaerobic glycolysis results in 2 pyruvate + 2 NADH and 2 net ATP. Is the whole anaerobic purpose of glycolysis to make the 2 net ATP? Then pyruvate and NADH are waste products? Also, pyruvate then reduces to lactic acid. What is the need for this? NADH is oxidized to NAD+. How is NAD+ used? Also, lactic acid is eventually converted back to pyruvate through Cori cycle. How is that pyruvate used?

I have altered your question to indicate that it applies to anaerobic glycolysis.

Anaerobic Glycolysis
As this question refers to glycolysis in the context of lactic acid fermentation it clearly relates to anaerobic glycolysis, which is why I added that to the question.
I believe it is correct to regard the primary purpose of anaerobic glycolysis as being to generate ATP for the anaerobic organism or tissue.
To understand the roles of NAD and lactate in this process you need to consider the chemistry. The conversion of glucose to pyruvate is an oxidative process, with the oxidizing agent being NAD+, which itself is reduced to NADH. For glycolysis to continue the NADH must be reoxidized to regenerate NAD+. This is the primary purpose of the reduction of pyruvate to lactate and is summarized in my own diagram, below.

So, the answers to your (paraphrased) questions “what are NAD and lactic acid needed for?” and “are they waste products?” are:

NADH isn’t needed for anything — it’s the consequence of the oxidative function of NAD+. No, it is not a waste product — it has to be reoxidized otherwise glycolysis would stop for lack of oxidising power.
Lactate also is not needed for anything, as evidenced by the fact that other reduced products of pyruvate are produced in different organisms, most notably ethanol in yeasts. Ethanol can certainly be regarded as a waste product, although the carbon skeleton of lactate is salvaged in multicellular oxygen-breathing organisms.

The so-called cycle of Cori & Cori
In my opinion it is best to approach glycolysis as I have done above, without reference to the tissue or organism, so as to understand the essential features of the process.
In the specific case of mammals, some tissues perform glycolysis anaerobically, e.g. the red blood cell (which lacks mitochondria) or rapidly excercising muscle (where the blood supply and number of mitochondria are not sufficient to generate ATP for muscle contraction. The liver, in contrast, has a plentiful supply of oxygen and hence NAD+, and so can reoxidize lactate to pyruvate if the former is transported in the blood from the anaerobic tissue to the liver, salvaging the carbon skeleton.
Under conditions of low blood sugar (e.g. starvation) it is important that the pyruvate be reconverted into glucose in the liver by gluconeogenesis, rather than be converted to other products, and the glucose is released into the blood. In this case one goes full circle, this process is generally referred to as the Cori Cycle. I always avoided this term myself in teaching students as I found it caused confusion with cycles such as the tricarboxylic acid cycle and the urea cycle, where all the chemical interconversions take place in the same tissue.
Footnote: Glycolysis under aerobic conditions
Under aerobic conditions (e.g. in the liver after a carbohydrate meal) the purpose of glycolysis is not primarily to generate energy but to utilize the glucose, storing it as fat (after glycogen capacity is reached) or using it to synthesize intermediates. There are different fates for the pyruvate (acetyl-CoA is shown), but lactate is not one of them as the NADH can be reoxidized far more efficiently in the mitochondria, with molecular oxygen being the ultimate oxidizing agent.

Text References
Berg et al. Section. 16.1 (5th ed.) covers glycolysis in great detail under aerobic conditions. The lactic dehydrogenase reaction is given little emphasis, but can be found in section 16.1.9.

You understood exactly what my question was even when I myself was confused about what my question exactly is. Thank you so much.  Your diagram helped. Now, I understand your diagram and why different steps are needed, but can you please help me understand the bigger picture. So the cycle in your diagram occurs when there is a lack of oxygen, i.e while exercising. But what happens where O2 is present (when we are not exercising) then there shouldn't be any lactate (b/c we dont get sore when we are sitting), if there is no lactate, means NADH doesnt get converted to NAD?

@JagmeetSingh — Happy to be of help. I've added a small section with a diagram indicating what happens to the NADH under aerobic conditions. The various possible fates of pyruvate (and glucose 6-phosphate) belong in an answer to a different question. If you have not yet met oxidative phosphorylation and the TCA cycle, then you will need to take your time learning about them — very important, but lots of detai.

So just to clarify: Glucose gets converted to pyruvate and in absence of O2, it goes through fermentation BECAUSE it produces at least 2 ATP(?), and when there is O2 available, it proceeds to carboxylation of pyruvate --> Citric acid cycle and so on. My only confusion now is that why does glycolysis need to occur (anaerobically) if it can not even proceed to cellular respiration.

I meant "decarboxylation" above and not "carboxylation".

Actually, I saved you some headache.
http://antranik.org/cell-respiration-part-1-anaerobic-respiration-glycolysis-and-fermentation/
This website it explained it well.

@JagmeetSingh — Note that under aerobic conditions in the liver there are at least two other pathways glucose may be metabolized by other than glycolysis. Also it is precisely 2 net ATP in anaerobic glycolysis — the ones generated through the capture of phosphate in the GAPDH reaction.

The whole purpose of glycolysis is to make the 2 net ATP, right?

No, actually it's breakdown of glucose as the name suggests, so as to provide pyruvate, whose fate depends on cells need and environment.

Then pyruvate and NADH are waste product?

Why? They are just intermediates which can be utilised in tca, or cori cycle or in any other metabolic pathways as cell needs.

Also, pyruvate then reduces to lactic acid. What is the need for this? NADH is oxidized to NAD+......

Wikipedia says:

The production of lactate is beneficial because it regenerates NAD+ (pyruvate is reduced to lactate while NADH is oxidized to NAD+), which is used up in oxidation of glyceraldehyde 3-phosphate during production of pyruvate from glucose, and this ensures that energy production is maintained and exercise can continue. (During intense exercise, the respiratory chain cannot keep up with the amount of hydrogen atoms that join to form NADH, and cannot regenerate NAD+ quickly enough.)
  The resulting lactate can be used in two ways:
  Oxidation back to pyruvate by well-oxygenated muscle cells, heart cells, and brain cells
  Pyruvate is then directly used to fuel the Krebs cycle
  Conversion to glucose via gluconeogenesis in the liver and release back into circulation; see Cori cycle
  If blood glucose concentrations are high, the glucose can be used to build up the liver's glycogen stores.

Also, lactic acid is eventually converted back to pyruvate through Cori cycle. How is that pyruvate used?

In cori cycle lactate is finally converted to glucose via intermediate- pyruvate.

In response to comments , relation between glycolysis and fermentation:

I think it would be nice if you add this picture: https://www2.estrellamountain.edu/faculty/farabee/biobk/BioBookGlyc.html (scrol a little bit down) , a nice graphical relation between glycolysis and fermentation

I didn't mean that figure, I meant the 3th figure @David

@RickBeeloo Is it correct now?

yes this will show the relatedness between fermentation and the need of NAD+ in glycolysis


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What disease does Saccharopolyspora erythraea cause?
For an examination assignment I have to find a disease caused by the bacterial species Saccharopolyspora erythraea, but I have searched the internet and have found no report of patients being infected with Saccharopolyspora erythraea. The only information I found on this bacteria is about its production of erythromycin.

I wonder whether the person setting the exam has made a mistake. For example in the paper describing the sequencing of the genome of this bacterium (Latin singular — bacteria is plural) all that is mentioned is its importance as a source of the antibiotic erythromycin.

The only mention I find for isolation of a related species in the same gents from a patient is this: https://www.ncbi.nlm.nih.gov/m/pubmed/19406809/ and it is not the cause of the disease there.

Yes sorry I meant I genus (T9 typing).

Welcome to Biology.SE!  I suggest listing the databases you have consulted — an expert might be able to help you based on knowing where you've looked either by confirming that you've searched exhaustively and that there is likely nothing to be found, or by directing to a source you might have missed.

@LazorLord. One possible source of confusion here is the change in naming and classification of micropolyspora within the family Nocardiacae, among whose species are the various nocardia responsible for 'nocardiosis'; which of itself is worthy of study.  Evidently certain members of this family are capable of arriving on Earth on meteorites.

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Why is it desirable to couple chemical production to growth?
I have the following question in systems biology:
a) Draw a graph showing the relationship of growth (Vbio) and Vefni for the system here. (Let the horizontal axis represent Vbio and the vertical axis represent Vefni)
My first thought was that it would simply be straight line from (0.5,0.5) to (1,0). But now I'm thinking that I have to take V4 into account as well.
b) Determine one or more reactions that are such that if they are taken
out the production of M4 is coupled to growth (growth-coupling). Draw a
graph showing the relationship Vbio and Vefni for the mutant.
Here I thought it would be V1 and V4. I'm not sure though because I haven't found a good explanation for what growth-coupling is exactly.
c)  Why is it desirable to couple chemical production to growth? i.e. what advantages do those systems have over the ones where no such coupling is present?
Here I have no idea.

What are the various terms supposed to mean? $V_{efni}$ etc.? I used the internet to translate and it looks like efni and aukaafur∂ mean respectively "stuff" and "byproduct" in Icelandic, but I'm not sure that fully explains the question. I guess $V_{bio}$ means biomass? The answer looks good but it's hard to puzzle out without this info.

Why is it desirable to couple chemical production to growth?

When designing new metabolic pathways for chemical production, one has to keep in mind that the purpose of it is to get scaled up (i.e. to reach industrial size).
From the industrial point of view, the faster/simpler a process is, the better. Growth coupled chemical production means that only one step is necessary in order to produce the desired product (before downstream processes). Otherwise, one would have to produce the biomass first (growth step) and then to proceed to the chemical production step. One step is cheaper and faster than two, not mentioning the intermediary steps that could be necessary (cells washing, centrifugation, filtration ...).
The main drawback of growth coupled chemical production is that the final yield ($mol_{final~product}/mol_{substrate}$) is hindered by biomass production. This can be a real issue if the substrate is expensive.


text:
Can humans distinguish light having the same color but different spectrum?
Can humans distinguish light sources that have the same color in RGB space but having different spectral composition?
I know one method, that is when the light is producesed by monochromatic laser, it looks "grained" due to interference, but this is a shape-based indicator. What about indicators not based on the visible shape, just on color perception?

flagged as "unclear what you are asking". Can you define difference between color and spectrum of light?

If by "same color in RGB space" you mean "activates human cones the same way" then the answer is no: color perception is based on the ratio that different cones are activated at. There is no difference between a spectrum that has a smooth distribution across wavelengths or one that is properly calibrated into three or more specific peaks.
This concept is why RGB monitors and TV screens work to produce just about every color (though there are of course limits to the spectrum that a RGB monitor can produce, but that is a technological limitation).

Yet, no electric lighting can emulate sun's light convincingly...

That's a completely different issue.

The "spectrum" of light refers to the relative power at each wavelength in the range of wavelengths of concern, in this case the visible wavelengths.
"Color" refers to the way we perceive various mixtures of wavelengths of light (that is, how we perceive the spectrum of light).  Most human beings have three types of light receptors (rods) in their retinas that respond rather broadly to three different overlapping ranges of wavelength (Short, Medium and Long) centered around 440 nm, 540 nm, and 575 nm.  Our brains receive neural impulses from the rods and interpret them to provide a perception of color.
The important point is that with only three types of receptors, our eyes are not able to distinguish the whole spectrum.  Our brains really just report the ratio of stimulation of the three different types.
OK, that's all background info.  I think the core of your question boils down to "Is there a way we can use our eyes to really perceive the spectrum of light?"  If there are no constraints, the answer is "yes".  For example, you can look at a light source through a prism or a diffraction grating, and it will let you see the whole spectrum. Each point of light will be spread out into a rainbow line, where each position along the line corresponds to a different wavelength of light.  There are other, more complicated ways, too.  If you would like to experiment with a diffraction grating, you can get one from, e.g., Edmund Optics.


text:
What species is the smallest bird?
What species is the smallest living bird in the world? What circumstances limit the bird size from the bottom?

There are definitely two questions here, and the question in the title and first part of the body should really be flagged for closure - it's easily googled - but the second is interesting and on-scope. Do you think you could edit it to the second part only?

this paper may interest you. minimum size may be related to maintaining their body temprature. https://www.journals.uchicago.edu/doi/abs/10.1086/282753

Related posts: https://biology.stackexchange.com/questions/21541, https://biology.stackexchange.com/a/66659

The smallest bird in the world is the bee hummingbird.
I think the minimum size is only limited by the size of organs. I mean that certain organs need to have a minimum size to maintain their function in the organism.

It is unclear to me how the "Wall effect" that you link under "organism" is relevant to your point. Is that an error?

The answered was probably thinking of something more like this, http://www.mrothery.co.uk/exchange/allkeynotesas.htm, but that is more of a limit on maximum size rather than minimum size.

@vkehayas yeah it is not much related to this topic. I quite misuse that it.

@L.Diago maybe update the link to reference Wikipedia instead, which not only gives the facts listed in your link, but also has pictures of them?

A better link: Bee Hummingbird.

I understand guys but that link was from guinessworldrecords you know. I  thought that it will fit better with the smallest bird in the world. :)

A complete answer should at least mention Kleiber's law.

I dont know but it doesnt fit to my answer.


text:
How to distinguish those flowers in outskirts: hawkweeds (Hieracium), hawksbeard (Crepis) and hawkbits (Leontodon)?
How to distinguish those flowers of the forest outskirts: hawkweeds (Hieracium), hawksbeard (Crepis) and hawkbits (Leontodon)?
I am not asking about concrete species it should be extremely hard since they have hundreds forms, but what are observable differences between genus?
I have read wikis articles but still not sure that I could distinct those flowers in the field right way.

http://en.wikipedia.org/wiki/Leontodon
http://en.wikipedia.org/wiki/Hieracium
http://en.wikipedia.org/wiki/Crepis

It's quite hard to answer this question and the best would be to follow a flora, which I'll not just copy informations from to past here.
So following are general observations subject to numerous exceptions.
Hieracium generally have lanceolate to oval leaves, not or little toothed, most hairy.
Crepis and Leontodon have generally Taraxacum-like leaves, that means, dentate to lobed.
Some Crepis have leafy stems (but some don't), while Leontodon always have their leaves concentrated to the base, forming a rosette.
[edit on 2014, october 2]
Be aware that there is another genus of the Asteraceae family which may be mistaken with the Crepis/Leontodon/Hieracium group, although it's easier to distinguish. It's the Hypochaeris genus.
Hypochaeris have few but not so homogenous species as there are within the other genera.
Hypochaeris radicata (which may be the most common species in France and wester Europe) have all its leaves basal, forming a rosette and sticking to the ground (never erected). These leaves are always lobed (neither entire, nor toothed), with erected hard hairs covering there upper faces.
Hypochaeris maculata may be mistaken with some Hieracium : it have hairy smooth entire leaves wich are (all or mostly?) basal forming a rosette.
[Addition on August, the 5, 2014]
Also Leontodon and Hypochaeris have hollow stem just below the capitulum(1). When you press the stem just below the capitulum, you fell it flattens under your finger, and if you use the nail to make an incision in the stem, you will see it is hollow like a pipe.

NB : Taraxacum also have hollow stems but they are fully hollow (from the base up to the capitulum), while Leontodon just have the upper part of the stem which is hollow.

Leontodon are almost always monocephal, that means, the stems are not branched : they have only one capitulum per stem, while Crepis and Hieracium and Hypochaeris mostly (if not always) have branched stems carrying several capitula.
(1) the capitulum is the type of inflorescence in the Asteraceae family. It's also called "head" (and actually, "capitulum" is the latin word for head).
You may like to have a look at this page [in french] presenting some common yellow and ligulate weeds from the Asteraceae family to get some illustrations of what I explained here.


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Why ravens play with garbage?
Why ravens play with small plastic details and other garbage?
Could you explain how this behavior was formed by evolution for birds-scavengers?

Ravens and other corvids are among the most intelligent birds. Of note, crows and ravens are known for their ability to solve problems that require tool use, memory, and delayed rewards (patience).
Many animals play, and ravens and crows are no exception. (A study entirely on raven nestling play.) The evolutionary purpose of play activity is thought to improve coordination/dexterity, provide exercise, strengthen muscles (such as wing-flapping by young birds that have yet to fledge), and develop social skills.
As to what type of objects ravens find most interesting to play with, I'm unsure of a definitive answer. Some birds, particularly the satin bowerbird, even collect colorful objects. My hypothesis is that the choice of object is likely due to simple availability (discarded) and conspicuous nature (color). In other words, ravens more easily find such objects because they are colorful, which in turn are frequently human-manufactured.

What is specific  in "forest scavengers life style" that pushed them to become most intelligent birds?

Quite a while ago I read "Mind of the Raven" by Bernd Heinrich, an expert in ravens. If I recall correctly, he suggests that ravens will essentially investigate any object they haven't seen before. Then after learning about these objects, they don't find them as interesting anymore.

@Eff An excellent book! Indeed chapter 24 is dedicated to play. I recall the same; I think it may also have been implied that investigating objects could contribute to finding new food sources.

@JYelton "I think it may also have been implied that investigating objects could contribute to finding new food sources." That's exactly what I remember being suggested.


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Assays during drug discovery
After researching the definition of Assay, I am left with the idea that an assay refers to scientific screening. It could be of chemicals, microbes, etc.
I understand that during drug-discovery assays scientists screen for chemical compounds that may make up an effective drug.
But could someone explain, or provide me with some links that further discuss the process of assays, or how they work or take place during drug discovery?
Frankly, I'm also still a bit confused about the definition of "Assay" itself.
Thank you.

I'm a pharmacy student and I can try to explain how they do to find new drugs.
In fact, there are many diferent ways to do so, it depends of what kind of new drug you are searching for.
Sometimes you're working on a disease which the pathological molecular mechanism of action are well-known and where many drugs are already effective. In this case, the 'assay' may just be about improving a well-known molecule by adding or changing a small part of the molecule (replace a ketone by an alcohol for exemple). Always in this case, you know on what molecular receptor you have to act, its 3D structure, its composition, its location in the human body and maybe the most important (but you don't know this every time and in this case, you could begin by this point) how and what part of your drug acts on any part of the receptor.
Then you have molecular libraries where you can search your new drug. They are alimented by different ways: someone who found a new chemical reaction that can add a chemical function where you could not before and generate several new compounds by applying his new method. All this compounds can be given to a national library where access is possible. You can also find intermediate compounds of reaction. This happens in public research because private laboratories keep their discoveries secret.
Sometimes you're working on a disease where the usual drug doesn't match really with the receptor, in this case, you have 3D tools that can modelize molecule and receptor in order to quantify how they match. This is achieved on many many molecule from this library and these methods generate few drugs that match the best.
Then you work on these drugs to improve them and make them compatible whith digestive barriers if you want an oral drug, or with the galenic form you need. This point is about improving the matching with the receptor by changing few parts of the molecule.
In fact when you know on which molecule you want to act, it all start with IT tools that mesure interactions between this molecule you want to act on and other random molecules.
When you don't know molecular mechanisms of your disease, you have to find it before, otherwise you're gonna work double-blind.
This is a few part of the reality, I hope that answered the last part of your question.

An assay may be thought of as a trial or test that is designed to quantitatively determine the amount of a substance in a sample.
Thus a biochemist might use a protein assay to quantitatively determine the amount of protein in a sample, or a pharmacologist might assay a sample to quantitatively determine the amount of drug present, or an enzymologist might carry out an enzyme assay to determine the amount of enzyme activity in a sample.
Let's take the case of the enzymologist. I take a liver sample, homogenize it, centrifuge and take the supernatant (soluble) fraction. I want to quantitatively determine the amount of a given enzyme activity.
I do this by performing a test by (say) adding a sample of the supernatant to a cocktail that 'does something' only if the enzyme of interest is present.  The 'do something' could be a color change, where the cocktail  contains  everything needed for the enzyme to work (all substrates, cofactors etc) and where the enzyme transforms one of the substrates to a coloured product.  I now have an enzyme assay which tells me if the enzyme is present (the trial), which may be made quantitative with reference to the amount of color produced in a given time.
As I remember things, Sherlock Homes was pretty good at the assays, using them to make trials of his geological samples, but I cannot find the quote.


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Using PGAL10 promoter to overexpress specific yeast genes: How to?
I was reading a poster about expression boosting for Artemesinin production in yeast and it had this line:

PGAL1
  and PGAL10 have been used for the
  overexpression of all genes from the mevalonate
  pathway.

What exactly does this mean? I suppose these are promotors? http://www.yeastgenome.org/locus/S000000224/overview
But how exactly does one use them during cloning to boost expression?
Say that you wanted to over-express ERG10, the gene coding for the first enzyme in the MVA pathway. How does one go about using PGAL10 to do this during the cloning steps?
Link to the poster: https://ddd.uab.cat/pub/tfg/2014/119349/TFG_narcisferrerledo.pdf

You're right about them being promoters, although it would be useful if you posted the link to the source of the sentence that you cite, so that we can read exactly how they are being used.
A fairly common way to study genes that aren't consistently highly expressed is to place them under the control of a strong promoter; that is, a promoter that is recognized by transcription factors in such a way that its linked gene is almost always expressed.
This is exactly what this group did in this paper, to study some features of yeast metabolism. In this case, the genes that they were interested in studying were cloned into a vector that was then inserted into yeast cells that lacked that gene. This way, the researchers knew that any expression of their gene of interest came from the vector and was driven by the pGAL1 promoter.
Similarly, if ERG10 was your gene of interest, this might be a strategy that you could adopt to study it.

I added the link to the source. It's a poster not a review, sorry. https://ddd.uab.cat/pub/tfg/2014/119349/TFG_narcisferrerledo.pdf

And this is a related paper: http://www.nature.com/nature/journal/v496/n7446/full/nature12051.html

From the poster, it looks like they're doing what I describe in my answer. That is, over-expressing a gene from a plasmid and driving that expression with a strong promoter. I think you'll see that a lot in studies like this one.

So how does one go about finding the actual DNA sequence for what they call PGAL1 / PGAL10. A search for these on Genebank / Yeast databases produced no hits.

Ok, maybe I did find the sequence! Would it be this one, you think? http://www.ncbi.nlm.nih.gov/nuccore/218616465


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de novo gene synthesis vs cDNA library creation from plant RNA: Pros & Cons
What are the relative pros & cons of the following two approaches when one wants to insert a known, sequenced plant gene into a target host organism:

de novo gene synthesis vs
plant matter extracted RNA converted to a cDNA library

Specifically my gene of interest is approx. 2000 base pairs so de novo gene synthesis cost works to about $350. (please correct my estimate if I'm wrong)
While this isn't cheap, collecting plant samples, cryopreservation, digestion, extraction etc. aren't easy either.
Any other considerations when / why one may favor one approach over the other?

Isn't "collecting plant samples, cryopreservation, digestion, extraction etc." also expensive? Think about cost and time. How long would it take to isolate the DNA vs synthesize it?


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Amount of variation between a canonical gene sequence in various samples
Suppose there is a GeneBank DNA sequence listed that produces a specific enzyme in a specific species of plant. e.g. A terpene Synthase.
Now if someone samples various trees of the same species would one expect to get the exact same sequence each time? Or is a certain amount of variation expected from tree to tree?
The drift behind my question is: Obviously not all tress of the same species are exactly identical in phenotype. So are the causative factors seen in sequence variations of various enzymes etc.? Or can we expect the various samples to have exactly identical amino acid / DNA sequences for particular genes / enzymes.
e.g.  e.g. Take this specific sequence: http://www.uniprot.org/uniprot/E3W202 If I sample from various trees of this same species and sequence this particular gene how much variation should I expect? Or would they be almost 100% identical?

It may or may not vary much. Unless you have additional information, it would be hard to tell. Try looking at conservation across different species. That may give some clue.

Is there a correlation between conservation across different species & within species variation?

Can't say for sure and I have not come across any study like that but conservation across different species can indicate that variation in the sequence may probably reduce fitness and same may apply for "within species".

Thanks @WYSIWYG I am surprised that there is no information of how much of a within species variation there is in enzyme sequence. I am having a hard time getting this info. too.

@curious_cat: I just stumbled across this: http://www.sciencedirect.com/science/article/pii/S2213596014001238. There it was found some conserved genes between humans and fruit flies in which there is substantial sequence variation within the respective species.

Your question is quite vague so I can only give you a vague answer saying what I would expect given only the information of your question.
The vagueness mainly comes from the huge amount of functional sequences in the genome, particularly also in enzyme-coding genes, each being more or less conserved. You say

I am surprised that there is no information of how much of a within species variation there is in enzyme sequence. I am having a hard time getting this info. too.

I would say that there is no feasible way of studying this question. You will find different selective constraints on every single enzyme and breaking this down to DNA this means that every single locus can be target of different selective pressures. And even if you figured out how to answer that question comprehensively for a given species (which probably will not happen), generalising it to every single species in every ecological niche, with every possible population history and so on is close to impossible. That is why one studies sequence diversity/conservation in model organisms and mostly on a per-gene basis.
In general, without knowing any background of a species and enzyme, I would however expect two things when looking at molecular variation between individuals of that species. These are merely based on general evolutionary principles and the nature of the genetic code. Keep in mind that these are trends, meaning that many genes will match these expectations but some definitely will not due to lineage-specific evolution.
First, I would expect generally high levels of amino acid conservation (but not always identity) especially in functional enzymes of core pathways. However, this depends on the function of the gene product. If the gene is a target of balancing selection, which maintains genetic variation within a population, there can also be considerable amino acid variation.
Second, there will generally be higher levels of DNA variation because of mutations with little or no fitness effect (synonymous variation or intronic variation which tends to have lower selective pressure).
To relate this to your last question: even though I would always expect a general amount of variation, even in the amino acid sequence of core enzymes, this variation will probably not be the main reason why you see different phenotypes. Phenotypic plasticity - the differential response of a given genotype to a given environment - is often stronger in plants than in animals as plants are stationary organisms. This plasticity will probably be the main cause of striking phenotypic differences between individuals.

Sorry about the vagueness. Can you comment on what parts I have left ambiguous so I can improve my question?  e.g. Take this specific sequence: http://www.uniprot.org/uniprot/E3W202 If I sample from various trees of this same species and sequence this particular gene how much variation should I expect? Or would they be almost 100% identical?

I did not mean your question was hard to understand. The vagueness comes from that there is no information on the species and the species' population history. This strongly affects the expectations of variation within a species. My answer are just some vague pointers what to think about. I will later think about if I have something more to add. :)

Thanks! I added some info. about the enzyme as well as the species so maybe that helps you formulate a more concrete answer?

To expand more: I know that there are homologous enzymes across species e.g. The enzyme or gene coding for (say) Squalene from its precursor will look similar with some regions changed. And BLAST etc. identifies this. What I am wondering here is within the same species but in different samples, how much variation is there typically in the sequence of the same enzyme.

@curious_cat: I added some further comments on the problem. In my view this is not really a biological problem but rather a philosophical one.

Interesting. I'm still not sure about your point. e.g. It should be a question entirely amenable to empirical study. Say, I take 100 random samples from one species & plot the variation in (say) 10 enzymes of interest I have one number. We do it for more species & now we have some picture. I'm not saying we will get one single number for a within species variation but it could be that mostly the similarity is 99%+. Or just 80-85%. But right now we just have no clue.


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Computing Percent Identity between DNA / Amino Acid Sequence
What are some tools where I can input a pair of DNA sequences (or alternatively a pair of Amino Acid Sequences) and compute a percent similarity identity metric between them?
Is BLAST the right algorithm for this or something else?
The context is that a certain patent protects all sequences at least 90% or more identity to a given sequence. I wanted to test some candidate sequences and verify the percent identity metric.
Below I post a patent-snippet where they actually define their identity metric.

tBLASTn, BLASTx and tBLASTx can be used.
It is clearly illustrated here.
If you have just two sequences you need not do a search against the database. You can simply align them using Smith-Waterman or Needleman-Wunsch algorithms, as David mentioned. However, you still need to translate your DNA to protein before doing the alignment. Again, as pointed out by David, with protein alignments you do usually not use identity. Scoring matrices like PAM or BLOSUM are used to calculate similarity.

If you want to compare two specific sequences that you already have, then BLAST itself is not the program you need. BLAST is a program that uses heuristics for rapid searching of a large database for sequences similar to a query sequence. Each of the highest scoring sequences obtained is ‘finished’ for presentation by running an implementation of quite different older and slower dynamic-programming algorithm, which is non-heuristic.
There is an option at the BLAST implementation at NCBI for just comparing two sequences, but this seems strange as one may as well just use the dynamic-programming alignment algorithm. Furthermore the output is not what you want as it scores a local alignment, whereas what your patent specifies is a global alignment (see below).
So for pairwise comparison of two sequences one normally uses a program that implements the Smith and Waterman dynamic programming algorithm for local alignment (only the regions of best similarity are compared) or the Needleman and Wunsch algorithm for global alignment (the whole of both sequences are compared). From your patent specification you clearly want a global alignment and a value for percentage identity.
You can find free web implementations of both of them at the EBI website (among other places) where the program ‘Needle’ performs the global alignment you require. Alternatively, there is an implementation of the Needleman and Wunsch algorithm at NBCI, tucked misleadingly into the BLAST suite.
I do see one theoretical problem with these programs in relation to the patent, although this may not matter in practice. The patent says that “The optimal alignment is the alignment in which the percentage identity is the highest possible”. But these programs try to find the ‘best’ alignment not on the basis of the highest identity score, but on the basis of the highest similarity score. This is done by using one of a number of emperical scoring matrices that encompass the likelihood of particular amino acid substitutions. For example a match between similar amino acids (e.g. Glu/Asp) may give a score of 4, compared with a perfect match score of 5. Moreover, a perfect match for an amino acid like Trp scores much higher than one for Gly. (More info on this and these terms can be found in the  Wikipedia Sequence Alignment entry or in the BLAST Glossary.)
Now you would expect that the ‘best’ sequence alignment obtained by optimizing for similarity in this way would also give the best identity score. This is quite likely for sequences of 90% identity or higher, but there is no reason it should necessarily be the case. In theory to get the highest identity score you should use a scoring matrix in which all perfect matches scored the same, and all mismatches zero. This is possible using an implementation of Needleman and Wunsch that allows you to use your own comparison matrix, e.g. this online EMBOSS-Explorer implementation. The problem is what score to give the perfect match (the average of match scores?), as this has to fit with the scoring penalties for mismatches. Or perhaps you should drop the mismatch penalty altogether, as you are only interested in the highest identity.
My advice would be to go for the Needleman and Wunsch algorithm, accept the defaults, and check you get the same score with different implementations. If your lawyers want anything more, I can offer a consultancy ;-).

BLAST does implement Smith-Watermann. The OP would still need to "translate" the DNA to compare it with the protein sequence.

@curious_cat if you have just two sequences then you can directly use Smith-Waterman or Needleman-Wunsch depending on what you really intend to do. With protein sequence you don't usually work with "identity"; you use scoring matrices like PAM or BLOSUM. In any case, the DNA has to be translated to protein in order to be compared with the other protein sequence.

@David The lawyers apparently tried to think this through. See the edit  in my answer. I post a snippet from the patent. It tries to address the question about how to score gaps. Now the question is how to get a score that matches this lawery-definition. Will BLAST out-of-the-box work to give a score matching their definition? They do recommend BLAST.

@curious_cat —Aaah. You mean identity. It seems counter-intuitive in plain English to talk about 90% identity, but that's the tech usage to distinguish it from "similarity" where you use a matrix of scores for different amino acid combinations. I'll do a test of my own and report back.

@David Thank you very much. I started a related thread here: http://biology.stackexchange.com/questions/48294/needleman-algorithm-for-optimal-alignment-of-two-amino-acid-sequences Would love your comments on that if you can!

@David Thanks. I've deleted a bunch of my comments too. I've kept a few that I thought added some relevant info.


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What is the advantage of having multiple pathways to activate complement?
We all know there are three pathways to activate complement: classical pathway, lectin pathway and alternative pathway. What is the advantage of having multiple pathways?

Although the initiating event of each of the three pathways of Complement (Clasical, lectin and alternative) activation is diferent, they converge in that all of them can cooperates with both the innate and the adaptative immune system to eliminated blood and tissues pathogens.
I think the major advantage is that when a individual has a deficient in a complement component  of ones these pathways the others can function to eliminate dangerous antigens or immunogens. However, if this complement component deficience is present in two pathways, patients can have the most severe clinical manifestation, suffering frequent severe bacterial infections.
Besides, these three pathway can function together to carry out a number of basic functions including:
Lysis of cells, bacteria, and viruses
Opsonization, wich promotes phagocytosis of particulate antigens
Binding to specific complement receptor on cel of the immune system, triggering activation of immune responses such as inflamation and secretion of immunoregulatory molecules that simply or alter specific immune responses
Immune clearance, which removes immune complexes from the circulation and deposites them in the spleen and liver

References please!

There can be many reasons for this, but generally redundancy in biological systems is very important in that it makes the system more robust. If one pathway fails, due to mutation or some environmental factors, the other(s) can compensate and the function of the pathway remains. In some cases it can also be used to tune the degree of activity or speed of activation.
Article on pathway redundancy


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What is this bizarre insect?
Well, a friend of mine sent me this picture of an creepy insect. I'm wondering if the picture is photoshoped or if it is real. It is said the insect lives in Indonesia, but I'm not sure.

Can anyone identify this? Thanks.

This is a Creatonotos gangis
This nice arctiine moth was described by Linnaeus in 1763.
The species  lives in South East Asia and parts of Australia.
C. gangis went viral earlier this year because of a post in The independent where they wrote about a facebook video on the species... I don't know if this is the same video that was popular at facebook, but take a look:
https://www.youtube.com/watch?v=hn1ms8qfqzM
Furthermore, I can tell you that those weird tentacles are in fact scent organs which secrete pheromones in order to attract sexual mates. And also, their larvae cause huge problems because they eat pomegranade leaves

Oh thanks, it is so freaky I thought it was a fake picture.

@Thai If I am not mistaken, these scent organs are called coremata (aka. Hair-pencils)


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Opening coverslip package
I feel pretty silly for asking this but I don't want to damage these coverslips.
I just ordered a 100ct box of coverslips and see no way to open them without destroying the container they are in. How are these little boxes typically opened? It seems smooth and sealed on all sides.

Looking at the container from the side, it's probably a situation like this:

There might be some clear plastic wrap around the entire thing as well that you would need to cut/break.

Thanks! I ended up using a knife to pry it open, turns out my fingernails weren't enough was all.

@Dilo You're welcome! Often times I can grasp both ends with just my fingers and pull them apart but it depends on how tight the fit is.

@Diio Thanks! I know how the package was built, but it just won't budge. I think it formed some kind of a vacuum. Pushing the cap up with a knife equally on all sides opened it, and subsequent opening is much, much easier.

Thanks for this posting. I was getting worried about my sanity. I pressed a knife edge hard on one of the sides, effectively cutting some plastic off. After that it opened w/o any trouble.

@peterd You're very welcome.

Basically the same answer, just explained differently... The top lifts off.  There is a tiny lip around the bottom edge (all four sides opposite the label). It's just a matter of getting a grip well enough to slide the top and bottom apart. (See diagram in last post, just imagine it vertically)
Thank you to the previous poster.


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Experiments on abiogenesis in laboratories
Has any scientist created an organism in a laboratory using the primitive kind of Earth's environment, like the one used by Miller, etc.?
I read that protobionts (coacervates and microspheres) have been created in the lab by Alexander Oparin and Sidney Fox respectively. I also read that these were not 100 percent living.

Abiogenesis is unrelated to evolution. It is not an evolution experiment (as we typically do with E. coli, S. cervisiae or D. melanogaster for example) of trying to recreate the environmental conditions of 3.5 billions years ago. You might want to remove the term evolution from your post.

As a start, you should read about the famous Miller-Urey experiment and the wikipedia page on abiogenesis esp. the section called current models.

@Remi.b I corrected the question's tags and title

Now the question you have is really very interesting and deep but the short answer is we still don't know enough to be able to decide
1.Precisely when an assembly of molecules and their interactions becomes a living organism and
2.We have no idea what the "alternatives" of what we know today as life are, so we can't be really sure what kinds of "other possible life forms" can be generated both in the laboratory and in the outer space on some distant planets.
In order to tackle the first question in the last decade or 2 new science has emerged-the field of synthetic biology whose goal is to "recreate" life in the laboratory from materials generally not considered to be alive-like cell membranes and DNA alone out of the cell but they are also trying to upgrade our current technology for manipulating the DNA of living organisms to the point where we can literally create new species in the laboratory. Here are some very good publications by the most renowned expert in the field of synthetic biology Craig Venter-here and here . These are seminal works for synthetic biology but if you want to know more you can search entire journals dedicated only to synthetic biology-here,here and here. There are actually hundreds of articles pertaining exactly to the answer of the question you are posing-what are the experiments we have done in the laboratory to recreate life in controlled conditions and how much we can "model" it to our own desires. Even if you only skim the abstracts of the articles in these journals you will be able to see how far we are in the de novo genesis of life and what we can do with our newest technologies to mimic the process by which the first cells arose. You would also find good work showing the prospects for manipulating current living cells to "synthesize" what scientists would consider new "man-made" species of bacteria. Although we aren't quite there yet the prospects are exciting at the least and really mind blowing at best. The discipline (I call it discipline because it isn't "just" a science but a combination of recombinant DNA technology, advances in the chemistry of large biomolecules, cutting edge genomics and proteomics, novel methods for computational modeling of metabolism and genomics and many more disciplines combined into one direction) is just in its "infancy" but even only what we can do now is enough to open the door for an entire new array of biotechnologies to come. However, I personally advise you to begin with the 2 papers of Craig Venter I already showed you and also this one and then go to these journals.
I would also recommend you seeing the reviews of Pier Luigi Luisi on the attempts of constructing self-replicating vesicles in the laboratory-here,here and here. He in my opinion is the man who has got the closest to actually achieving in the laboratory the synthesis of systems close enough to the living cell-self-replicating lipid vesicles. I think if we are ever to recreate life in the laboratory this is the closest shot we have. You might also be interested in this paper here and this here who pertain to the same field-the use of lipid vesicles as a simple way to recreate the origins of life and to build living cells in the laboratory.
Lately, there is also one brand new interesting paper from this year on the issue of creating molecules and systems of molecules capable of evolving themselves into more complex ones here.
Now on the second question-how to recognize what kinds of forms of life can exists in the universe, there is also a fast growing new science-the science of astrobiology whose goal is to devise a broader perspective on what life is. can be and how it can arise in the wide context of the cosmos. not only in the particular context it occurred here on Earth. There are 2 good journals pertaining to this field here and here which can give you very good perspective as to what the field is about and how it can shed more light both on what life generally is in the universe and how can we recreate it on Earth. I would also recommend you to read the articles Life as we don't know it, Defining life,How rare is complex life in the Milky way? and The potential of detecting "Life as we don't know it" by fractal complexity analysis. Those papers should be nice "introduction" to the world of astrobiology and if you follow through browsing the journals I just showed you can get a pretty good idea where we are today in the quest to answer your question.
You might also want to consider learning more about the origins of life. It also is a field directly related to the question you posted. Nice review on the topic is here and you can also check out this article and this article here. Then, you may want to check out the journal dedicated specially to investigation on the origins of life-Origins of life and evolution of biospheres and watch this online lecture on the subject.
Another issue pertaining to the question is the definition of life and how difficult it is to be formulated. If you become familiar with the issue you will understand why it's so difficult to tackle the problem of how to synthesize life, where it is throughout the universe and how it originated here on Earth. I recommend you these 2 seminal works on the definition of life here and here. But I would also recommend you to read this,this and this article to get a deeper look at the problems we face even defining life today. If we can't even agree on what life is how do you expect to be able to understand how it originated or how to create it?
Another direction you could also look at is our attempt to model and describe what we can call life at all levels it can appear-the field of artificial life. You can learn more about it in the journal Artificial life which deals with our attempts at modelling complexity in abstract systems close to the dynamics of the living ones. Yet another attempt at understanding the dynamics of the living is the interesting field of biosemiotics about which you can read short overview or get more accustomed into in its journal here. I think this list is more than enough to cover all the major directions your interests can take you on.
But to get "the bigger picture" of the question here you need to do much more than that and to follow virtually every publication pertaining to the definition, origin, synthesis and location of life throughout space and time and this can be daunting task, believe me, I do it every day since years! But despite the enormous quantity of papers and articles I go through there are always newer and newer things to discover and no matter how many hours I dedicate to this task and how much it fulfils me there are still gaps in my knowledge and am learning new things about different perspectives on the BIG question-What is life? all the time!
So, to give you an advice derived from personal experience-the question you tackle is really very interesting and fundamental one but even if it consumes all your time and efforts you would still not be able to follow everything which can be pertained to it, so my advice is to take only 1 or 2 approaches used in either of the fields I just described you and concentrate only on their keywords to follow the advances of the people behind them. Take something from synthetic biology, something from the origin of life field or something from astrobiology and visit the journals I just showed you from time to time to search with these keywords and see what is new. Then you would have good enough idea how close we are to synthesizing life in the laboratory and knowing more about its nature and origins. This is my long answer and the best advice I can give you.
Hope it helps :)

Wow, this answer got the size of a small paper itself! At least, I hope here are enough references and advices for everyone who wants to explore the field. The least, it took me a hell of an effort to write it.

Synthetic biology and abiogenesis are not synonymous and treat very different issues in biology.

@BryanKrause , I agree they aren't synonymous but I disagree they treat very different issues in biology. If you browse the 3 journals I just give you above with the journal Origins of Life and the Evolution of the Biospheres (done it in the past) you would see keywords like synthesis of living organisms, minimal genome, minimal set of proteins, of metabolic reactions and other "minimals" coming from both of them. The same is true if you browse The Journal of Theoretical Biology and Biosystems with the same words. For me it means different fields. the same problem. How's that for an answer?

How my God, there is lot's of things to learn and to know, and it really helped me, it's very crazy to think about creating life and your answer gave a picture of it.

@YordanYordanov Synthetic biology is mostly about figuring out what are the minimum necessary requirements for life, taken from modern (in terms of evolution) organisms, and assembling them together with modern (in terms of human technology) means. There is a practical side to this approach, but on the scientific side it is really about understanding how extant life works. Abiogenesis is about the creation of life from an unorganized soup mimicking possible early stages of life on earth and might produce life that is nothing like what it has evolved to.

@BryanKrause , how do you suppose we will know when what we have produced is alive if we don't first develop clear picture of when something becomes alive. And here is where synthetic biology comes it. I will argue that precisely the definition of Life is where the fields of origins of Life and synthetic biology meet so there is a good reason to follow them both if we want to create Life. First is the bottom-up, the second the top-down approach to the same question. Here is where they meet and they can "work out" the problem together.

@sreekara , actually I don't think creating Life is so crazy as it seems and may be one we will be able to it on regular basis, but for now as you can see there are too many gaps in our knowledge to be anywhere near it. So my advice is, if you are really interested in the field, to take the list of the journals I provided you and browse them every once or twice in the month to see what is new. Then you will have good and updated enough idea what is going on in the field and how close we are to this task.

I personally am much more passionate about this question, this is why I follow everything almost every day but unless you want to specialize in the "big questions of Life", e.g. what it is, when it arises, what is its minimal organization and how it evolves you don't need to do it. It is something that can really take up all your time and even there you won't be happy with the results. I know the field pertaining to this question well because it is essential part of my specialty but if you don't want to go deep into the theory of biology there is no need to spend so much time and effort.

Coacervates are electrostatically separated colloidal droplets. Colloids are a suspension of insoluble particles in a liquid medium. Oparin proposed that ionized organic colloids in an could interact in such a way as to form a 'metabolism' thus acting as a precursor to life. Oparin was never able to test his thesis in any way, but the Urey-Miller experiment was a partial vindication, showing that the complex organic molecules necessary for his thesis could be formed inorganically.
As opposed to Oparin, Sidney Fox based his work off the results of the Urey-Miller experiment. He addressed the next problem, that of how the molecules synthesized in the Miller-Urey experiment could develop into cells. His research into microspheres, showing that they could form 'protocells' in inorganic processes, and that they could undergo binary fission, lead him to believe that microspheres of organic materials were the precursor to cells.
If you combine microcells with coacervates, you can explain how a cell developed its form and metabolism, thus generating life.
I am not really in a position to judge the accuracy of their claims, but as far as I can tell, while there are other theories of how life formed, neither Oparin or Fox have been categorically disproven. That is the say, while there are many theories on the specific set of conditions that caused the initial formation of life, the theories of coacervates and  microspheres are critical components of many theories.
That is the background on abiogenesis research with respect to Oparin and Fox (and Miller-Urey). Regarding the specific question, 'Did any scientist creat a organism?' the answer is most certainly, no. There have been amino acids created, but no metabolism or anything that could be construed as 'life.'

@,kingledion thanks for your answer, I got to know more...

Actually, I think it is quite a haphazard answer. Just posting Wikipedia link and mumbling few words how little we know is NOT in any way near what the current situation is. If you are truly interested in the emerging science of "creating life" you should google for the term synthetic biology. There are entire journals dedicated to it! This is a good place to start. Also see the work of Craig Venter-he is the first man to claim trying to build living cells "out of scratch" in the laboratory. Here is a list of his work-http://jcvi.org/cms/about/bios/jcventer/ I suggest you pay special

@YordanYordanov It was helpful to the asker. If you know more, why don't you write a more helpful answer?

attention to this article-https://www.ncbi.nlm.nih.gov/pubmed/20488990?dopt=Citation You can also check the works of Pier Luigi-Luisi and a very good publication by Lauterbur-https://www.ncbi.nlm.nih.gov/pubmed/18290757 which is precisely linked to the subject you asked-when chemistry becomes biology. There is also a whole YouTube lecture course on the origins of life you can see here-https://www.youtube.com/playlist?list=PLguiSpvMdqIX_BP-dsPzpjrfia60NLwae&spfreload=5 . I think these links will be very helpful for you

I'm a kind of a "great fan" of the field but I will need some time to organize all the links I have here, it will take some time to find everything I have here on my computer to its proper source on the net But I'm onto it, don't worry. Can you wait for about 30 minutes?


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Hybridization in Darwin's finches is rare or frequent?
I've talked to a couple of researchers today and read recent articles on the subject of hybridization of Darwin's finches. I'm confused about the consensus in the scientific community.
First, I was reading about hybridization in systems where adaptive radiation occurred. I came across this Honeycreepers paper: Knowlton, J. L., D. J. Flaspohler, N. C. R. Mcinerney, and R. C. Fleischer. 2014. First Record of Hybridization in the Hawaiian Honeycreepers: 'I‘iwi ( Vestiaria coccinea) × ’Apapane ( Himatione sanguinea). The Wilson Journal of Ornithology 126:562–568.
In this paper they are saying:

The Galápagos finches, for instance, hybridize frequently both within and across genera (Grant et al. 2004, Grant and Grant 2008).

But in the resources they cite, here is what I found:

Rare hybridization between the species, occurring partly as a result of misimprinting on song (Grant
  and Grant 1998)

From Grant, P. R., B. R. Grant, J. A. Markert, L. F. Keller, and K. Petren. 2004. Convergent evolution of Darwin's finches caused by introgressive hybridization and selection. Evolution 58:1588–1599.

Hybridization was rare at the level of individuals: only
  a few percent of all offspring are hybrids

From Bell, G. 2015. Every inch a finch: a commentary on Grant (1993) 'Hybridization of Darwin‘s finches on Isla Daphne Major, Galapagos’. Philosophical Transactions of the Royal Society B: Biological Sciences 370:20140287–20140287.

Hybridization was always rare.

From Grant, P. R. 1993. Hybridization of Darwin's Finches on Isla Daphne Major, Galapagos. Philosophical Transactions of the Royal Society B: Biological Sciences 340:127–139.

Hybridization occurs rarely (less than 2% of breeding pairs) but persistently across years, usually as a result of imprinting on the song of another species.

In Grant, B. R., and P. R. Grant. 2008. Fission and fusion of Darwin's finches populations. Philosophical Transactions of the Royal Society B: Biological Sciences 363:2821–2829.
Did I miss something, or is hybridization rare and not frequent? Maybe frequently is so vague that it includes, rare?

I actually just had to read a Grant & Grant paper, so hopefully, I can get this right. My understanding is that hybridization events have repeatedly seen to occur, but the events themselves usually do not repeat within a lineage, i.e. once a lineage becomes partially hybridized, it is unlikley to continue to breed with adjacent populations.
Due to the reproductive barriers that come from song patters of hybridized individuals (Grant & Grant, 2009), Repeated hybridations are unlikely to occur within a lineage, even when in the presence of a species with which hybridization can occur.
Grant, P.R. and B.R. Grant. 2009. The secondary contact phase of allopatric speciation in Darwin's finches. PNAS 106 20141-20148

Please cite the Grant & Grant paper. We strongly encourage the addition of sources here at Biology.

That's what I was thinking: "Galápagos finches have very low, but persistent, levels of hybridization events, compared to other system where speciation is near completion or completed or where there is high reproductive isolation" For the actual numbers and percentages of hybrids see: Grant, P. R. 1993. Hybridization of Darwin's Finches on Isla Daphne Major, Galápagos. Philosophical Transactions: Biological Sciences 340:127–139.


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What are the effects of enzyme exposure to high temperatures?
Question: After enzymes are exposed to high temperatures and undergo denaturation, then returned to their optimal temperature and renatured, can the enzyme's active site return to it's original shape and will it function at the same level of efficiency as it did before being denatured and renatured?
Some background I wrote to the question:
I am just beginning to learn Cell Biology, I hope what I've written is correct.
When you raise the temperature of an enzyme, at first it will increase the efficiency of the enzyme's activity, but eventually as the temperature rises, the enzyme with stop functioning and undergo denaturation, which means that the 3D formation of the protein is unraveled, so it doesn't function anymore. From what I've managed to research, the high temperature changes the shape of the active site in the enzyme, which is what allows the enzyme's activity in the first place.
I know that some proteins cannot be renatured (like adding heat to an egg will fry it and there is no way to unfry it), but some can be renatured (like heated milk, when it cools down the protein bonds will reestablish themselves).
But will the enzyme's active site return to it's original shape and manage to function at the same level of efficiency as it did before? Or is the damage permanent?

Possible duplicate of How does temperature influence the rate of protein degradation?, How is the rate of transcription influenced by temperature?, and Influence of temperature on protein binding and decay rates.

The answer is that it completely depends on what specific enzyme you're talking about; some of them will and some of them won't. What you wrote is correct, that increasing temperature of most enzymes (although there are exceptions) will increase their activity to a certain point, after which the proteins lose their 3D structure and become unfolded.
Upon cooling, it all depends on whether the enzyme can re-fold by itself or not. Some proteins when heated form aggregates, which are more stable than the original conformation, and so generally won't refold with cooling. Some proteins are able to fold into proper conformation by themselves, while other require assistance from chaperone proteins in order to fold correctly. Many of these chaperones are called heat-shock proteins, which are upregulated in response to thermal stress. That points to the fact that many proteins can't just refold on their own, and require help to regain their original conformation from these HSPs.
So the real answer is that it all depends on the specific protein. It also depends on how much you heat the enzyme, and how much of its 3D structure you affect, if you only partially denature an enzyme, it's more likely to refold than one that's been completely denatured. However, if you want an answer about enzymes in general, I'd say that most enzymes after denaturation aren't able to refold properly and regain their enzymatic activity, so the damage is permanent.

Thank you so much! Your answer really helped and gave me some more knowledge to use, to do further research into the matter.


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Deducing protein sequence length from gene DNA sequence length
Is there a standard way to deduce protein sequence length from gene DNA sequence length of the gene coding for it?
Naively I had assumed that amino_acid_seq_length / 3 -1 (deleting one for the stop codon)ought to work but apparently not always. Is there a better way?
Let's assume the gene is eukaryotic, specifically a plant gene.
e.g.

Or

(AA Seq. / 3 ) - 1 should be a good approximate in bacteria and archea. Since generally transcript RNA is mature. In eukaryotic orgsnism you have all sorts of processing complexity,  so unless you intron spliced sequence, you wont know for sure the protein sequence

Thanks @SciEnt. But if you express a eukaryotic gene in something like E Coli the resultant recombinant protein should still be (AA / 3) - 1 since they will lack the post-processing machinery?

curious_cat, if so that is what we would expect, you are correct.

If you look at the DNA sequence in the patent, you will see that it does not start with ATG and does not end with a stop codon. The disclosed sequence has some additional bases in it, therefore the discrepancy in protein and DNA length. Those additional bases almost always occur in cDNA, e.g. because of polyadenylation, Kozak sequences, etc.

Thanks! So, if you were to want to use the sequence for (say) heterologous expression would it be imperative to correct those aberrations? i.e. How does one infer what the right length of the Amino Acid will be or which bases exactly are the additional bases? In other words, how does one "clean up" a cDNA sequence?

You can use a tool like this one: http://web.expasy.org/translate/ Just enter the sequence and look for the longest open reading frame.

Thanks again Ashafix. That explains a lot to me. One small question: Your tool predicts the correct 569 AA protein in the case of my second snippet. That's great. But in the case of the first sequence the tool gives 569 whereas the patent snippet lists 570. http://web.expasy.org/cgi-bin/translate/dna_sequences?/work/expasy/tmp/http/seqdna.6001,2,2 Any idea why I'm off by one AA? Am I making a mistake? Or....?

Seems like patent data obfuscation to me, the actual sequence in the patent is 569 but if you look at the last 5 amino acids in the translated sequence, it is PLGEE, while in the patent amino acid sequence a aspartate appears out of nowhere:  PLDEE. Two recommendations: 1) Start organizing your sequences with some program, it is easier to visually compare them 2) treat patents with caution, they have to tell the truth otherwise they will be invalid, but they don't necessarily tell the whole truth and it might be hidden deep in the patent to confuse the reader.

Thanks for the tips! Any recommendations for a program to organize my sequences? What do you use?

I don't think it is appropriate here to recommend commercial software but on Researchgate you should find plenty of hints.


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Relative concentration of enzyme vs reaction product
I was reading a paper in which a recombinant protein (His-6 tagged) is expressed in E Coli (BL21 DE3). The yield of the enzyme isolated from the culture is reported as 10-30 mg per L of bacterial culture. (After purification by Ni-affinity Chromatography)
First, is this a reasonable concentration for an enzyme? I thought it was rather high.
Second, when they measure the concentration of the product of the enzymatic reaction that was found to be merely 1-3 mg/Litre of bacterial culture.
Is this typical or unusual for the product concentration to be an order of magnitude smaller than the enzyme concentration? I assumed that since enzymes were in catalytic amounts they ought to be at lower concentrations?
PS. They use SDS-PAGE followed by the Bradford method for determining the protein titres. How accurate is the Bradford method?

Remember that the concentrations you report are in mass units rather than mole units. If the protein has a mass of 40,000 Da, reasonable for many proteins, then 20 mg/liter means $0.5$ x $10^{-6}$ mol/liter. A typical small-mass product of an enzyme reaction might have a mass about 200, so its apparently lower mass concentration of 2 mg/liter is $10$ x $10^{-6}$ mol/liter, 20 times higher than the enzyme concentration in terms of numbers of molecules per liter. The mole or molecule ratios are what you should think about in terms of catalytic function.
Furthermore, from what you provide we don't know whether the enzyme was produced under circumstances that allowed it to express its activity; there may have been limitations on substrate availability, presence of inhibitors that would be removed in later purification, and so forth. In this scenario, evidently to obtain enzyme for downstream use, the emphasis is typically on getting large amounts of the specific enzyme regardless of whether some reaction product is formed. I don't find the enzyme concentration particularly high for something that the investigators are trying to over-express as in this case.
The Bradford reaction is a mainstay of standard biochemistry, as it's simple and straightforward. Different proteins can bind the reagent to somewhat different extents, so there is a second-order issue of whether the protein used for the standard curve and that being measured are similar enough in that respect. In practice, what's important is to provide enough information in the methods that are described so that someone could repeat the work to determine the relation between the Bradford measurement and some other more accurate method for this particular protein.

Ah! Yes. I blundered. Totally forgot about converting to molar concentrations. My bad!

Also, the enzyme  mass is approx. 60,000 Da & the reaction-product is MW=200. So your guesses were bang right on target! :)

Funnily, neither the paper nor the supplementary information seem to give any details about the method they used for enzyme quantification. Other than that they used the Bradford method.

@curious_cat, mass versus mole confusions are easy to make. They become less frequent with practice, but can still occur. For the Bradford method, I would generally assume that bovine serum albumin was used as the standard if it wasn't specified. If a particular manufacturer's version of the Bradford test kit was specified, the kit itself might have a standard protein that the manufacturer's information would disclose.

Thanks Ed. If I may ask two follow up questions: (1) What would be the more accurate (than Bradford) methods you refer to? & (2) Your answer seems to indicate that the conditions for max enzyme expression can be / are different than those for max product synthesis. Am I interpreting this correctly? If yes, can you comment in what way are these conditions typically different?

With respect to issue (1), the gold standard is to purify the protein in large amounts and weigh it, then use that batch of the protein as the standard for other assays whether colorimetric, mass spectrometric, or based on binding to an antibody (e.g.,ELISA). Stable-isotope labels can also be used along with combinations of liquid chromatography and tandem mass spectrometry for absolute quantitation of a protein that has been digested into smaller known peptides. See this Wikipedia page as an introduction.

For issue (2), it is in principle possible to express an enzyme in a cell-free system that contains no substrates for the enzyme. That's not as efficient as bacterial over-expression, but the principle is the same: you don't necessarily have to produce product from an enzyme just to get the enzyme itself expressed. In fact, a non-hydrolyzable mimic of an enzyme substrate, IPTG, has been used for decades to drive expression from the lac operon that naturally controls $\beta$-galactosidase production.


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What species of fox is this?
I found this picture of a fox in a news article about arctic foxes in Sweden (source), but I'm not sure whether it is actually an arctic fox.

On the one hand, it has white fur, which is the correct winter coat for an arctic fox. On the other hand, the fox's ears do not have the distinctive shape of arctic fox ears, but ears that look more like red fox ears.
The image credit given by the article is just "iStock", so I searched iStock to see if I could find more information about the photo. I found another photo of the same fox here, also labeled as an arctic fox, but not really any further information.

What species is this fox?

It tells you in the source!

@PichiWuana I have only the word of iStock's tags to go on, and that's not exactly trustworthy in an unclear case like this. I have seen images on that site be tagged with multiple species names before.

This is a white morph red fox, not an arctic fox.
As noted in the question, this fox has larger, more pointy ears than an arctic fox, and the second picture shows it to have a longer muzzle as well.
Another clue is that these pictures were taken in the springtime or early summer (which you can tell from the new growth on the plants in the picture), and that arctic foxes are only completely white during the winter. During the spring, an arctic fox should look like this:

You can also easily tell that the fox in the picture is not an albino, because of the dark pigment in the nose and eyes.
The red fox has quite a few different color morphs, and this fox looks to be a white color morph.

In that diagram, this fox would be labelled as leucistic (white).
Here are some other white morph red foxes:

I like how your profile picture matches the subject of the post. +1 for the good answer


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Small, brownish bird with reddish spot around eyes

This bird was seen in the Bourgoyen-Ossemeersen nature park, Ghent (Belgium) on December 3rd 2016. It is about the size of a common chaffinch.
We couldn't get a very good picture of it, unfortunately. What is the species of this bird?

From the the tree ("aulne" in French, with very typical fruits), I would have bet on this bird: https://fr.wikipedia.org/wiki/Tarin_des_aulnes, but is is true that the individual on the left looks much more like /Fringilla coelebs/.

It's a Chaffinch (Fringilla coelebs). From the first picture you see the
greyish head and orangish chick. From the second picture the typical whitish/greenish
wing bars. From the third pic the bricky belly.


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How does blue, yellow and orange coloured light affect photosynthesis?
I've been conducting an experiment with different colored light and photosynthesis, and so far my hypothesis states that red light will grow the plant, green will slow or kill it, and white will grow it as normal.
I'm wondering what would happen with blue, yellow, and orange.
Thanks.

You know what they say, do the experiment and find out. Just remember to include controls.

Your thought process should revolve around optimal spectrum for photosynthesis, since whether that happens sufficiently will determine the health of your plant. Just poking around, I found this document.
What light will be usable for photosynthesis depends on which version of light absorbing protein is being used to capture energy from photons.
This diagram would indicate that pure yellow would be pretty ineffective for any pigment. Blue is fine, as is darker orange/red for chlorophyll A and B.
Keep in mind that a lightbulb, unless a very special one, will still have lots of other spectrum bleed.  It won't be a pure single color (even though it may look like a single color to your eye).

Another source from Khan Academy.