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Advantage of opponent color?
Opponent process is a color theory that states that the human visual system interprets information about color by processing signals from cones and rods in an antagonistic manner (source).
What is the advantage of opponent color against RGB color? For example, in object recognition or edge detection?
Can we say that it provides some level of invariance to changes in brightness?

RGB color is a more direct representation of the "raw input" received by the (human) eye, since the three types of cone cell have responsivity spectra that roughly correspond to red, green, and blue light:

Opponent color decomposes color into three "dimensions" of opposing properties: dark or light, yellow or blue, and red or green.  This provides some brightness invariance, since changing the intensity of light will change the brightness but not the yellow/blue or red/green balance of the color, even though the stimulation level of all three types of cone cell will change.
One could speculate that opponent color perception is more "meaningful" in real-world environments.  The dark/light axis represents the overall amount of light, the yellow/blue axis indicates which end of the visible spectrum is predominant, and the red/green axis provides a finer distinction for low-frequency light.

"...even though the stimulation level of all three types of cone cell will change": The stimulation levels change, but the ratios of r/g/b/ cone activation remain the same under varying luminance, regardless of the opponent channels. Hence opponency is not necessary for color constancy.

and why would 'end-of-spectrum' information of the yb axis be helpful?

@ChrisStronks Of course color opponency is not the only way to achieve color constancy, I'm not sure what your point is.

@ChrisStronks  The "end of spectrum" information is helpful in finding fruits or young leaves among other foliage.  This is thought to be why trichromacy evolved in primates (most other mammals have only two cones).

Trichromacy helps in fruit recognition  for sure, but the added color is either red or green, the dynamic frequency range wasn't changed much when trichromats appeared. See the benefit of trichromats and fruit in this answer: http://biology.stackexchange.com/questions/24481/is-our-color-vision-calibrated-to-sky-vegetation-and-blood/24544#24544

@ChrisStronks Sorry, I misunderstood what you were asking.  The blue/yellow axis represents whether the light is predominantly high-frequency (more blue) or low-frequency (more yellow).  This is the most basic type of color vision and is helpful because color provides useful information about the world.

I know... My points are (1) opponency is not involved in color constancy (rgb regulated) and (2) yb / dichromatic vision / end-of-spectrum / dynamic range have not much to do with the advantages of color opponency. The fruit hypothesis can be explained at the cone / rgb level.

Let us continue this discussion in chat.

The first question, namely what is the advantage of color opponency 'against' RGB, is technically incorrect. The opponent system (Red/Green; Blue/Yellow and brightness channels) is physiologically situated in the neuronal retinal layer and higher visual structures such as the lateral geniculate nucleus and receives input from the RGB system (photoreceptors in the retina: Red, Green, Blue cones).

Then the question becomes "what is the advantage of adding the opponent channels on top of the RGB system? The advantage of opponency may in fact not be the negative opponent effect so often stressed in the Hering model (and shown in the figure: e.g., blue suppressing yellow etc). The advantage lies in the finding that activity of one opponent pair increases activity of the opponent color in adjacent areas in the retina. This effect results in a sharpening of color contrasts between the opponent colors (Hurvich and Jameson, 1957). Indeed, the poor spatial color-contrast, as provided by the sparsely placed cones in the retina, is enhanced by this mechanism. Especially the blue cones are present in isolated patches in the retina. Because one color in an opponent pair increases the other's activity directly adjacent to it in the retina, the resolution of the blurry retinal image is greatly increased. Hence, as you rightfully say, edge detection and in particular color contrast perception is enhanced.
Object recognition, as you mention in your question, is a process that is facilitated by the visual system through many stages including the higher visual cortices. Enhanced color contrast will likely facilitate object perception, but indirectly since color contrasting makes up just a small portion of a much bigger and complicated neural system devoted to object recognition, namely the visual 'ventral' stream (Ishai et al., 1999).
Lastly you ask whether opponent colors may facilitate invariance to brightness. Assuming you mean color invariance under varying luminance (referred to as color constancy) the answer is no. The RGB cone system can deal with this easily, as the ratio of cone activation yields enough information to code the hue under various luminances. If a certain object reflection activates twice as many red cones than green cones, it will also activate the same ratio when the luminance is increased (Mather, 2006 - Chapter 12).

@AliceD, could you expand on the last point please - why do you think the opponent process does not facilitate color constancy? You're saying that 'RGB cone system can deal with it easily by calculating the ratio of cone activation', - but the opponent process is exactly that, the calculation of the ratio between cone activations. It just so happens that our particular visual system does this via the R-G, B-Y, Brightness variables.

The opponent process is indeed useful for color constancy.
Opponent process maps RGB (or LMS) coordinates to YB-RG-WhiteBlack coordinates:

RG axis, for example, is calculated by the simple algebraic R - G (or L - M).
If the brightness is reduced, there will be fewer photons falling on both the R cones and the G cones.
The WhiteBlack value will change:
R + G + B = ?
8 + 3 + 0 = 11 →
7 + 2 + 0 = 9 →
6 + 1 + 0 = 7 --- notice WhiteBlack value changes

The difference between R and G will remain the same:
R - G = ?
8 - 3 = 5 →
7 - 2 = 5 →
6 - 1 = 5 --- notice RG value stays the same

This ensures color constancy - the visual system has a way to determine that the color of the object didn't change, only the illumination did.

Here is a related quote from Vision Science: Photons to Phenomenology by Stephen Palmer:

The opponent representation is more useful because it helps determine which
differences between adjacent retinal regions result from changes in
the level of illumination (such as when a shadow falls across a
surface) and which result from changes in spectral reflectance (such
as when a surface is painted two different colors). Changes in the
amount of illumination will generally just raise or lower the overall
amount of light (that is, change the output of the B1/Wh system) while
the chromatic balance remains constant (that is, the outputs of the
R/G and B/Y systems are invariant).

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The skin color of bonobos
Why is that bonobos skin color on the areas not covered by hair are dark throughout life unlike the chimpanzee?

"disprove the idea that skin color evolved".. How is this related to evolution?

I removed it. If it wasn't related then excuse me.

Most likely they're different because ... they're different. Chimps and bonobos are separate species, and have evolved many different traits from each other over time. The difference in skin color may have evolved as an evolutionary advantage of some sort (maybe bonobos spend more time in direct sunlight than chimps), or it may just be an artifact, or side effect of some other mutation.

source: Stack Exchange

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sort: votes


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How do CO₂ and carbonic acid (H₂CO₃) work in buffering the blood?
Been struggling with this for the past few days even after reading half of the acid base tutorial here, if someone could help me that'd be great.
What I don't understand is how HCO3- is supposed to buffer the blood. I know that HCO3- is a base and can accept H+, but the way that the HCO3- came to fruition is by donating a H+ to the surrounding water, so there's a net zero change in H+ thus no buffering action took place. Let's say a HCO3- accepts a H+, now the CO2 produced by H2CO3 → CO2 + H2O leaves the blood because the PvenousCO2 gets higher than the CO2 pressure in the air in the lungs, and you exhale. Now you're in the exact same situation as before the CO2 got attached to H2O.
Still the text calls it as an buffer, with a very large buffering capacity as well. How does this work?
To me it seems that buffering blood using HCO3- makes as much sense as using HCl, Cl - can accept H+, right? Nevermind that HCl is a very strong acid.. Surely no one would think of using HCl to buffer blood.

I just have one question for you. If the body could regulate the amount of HCO3-, in effect generating new buffer, would that help you to understand how it is the major buffer that it is?

maybe, not sure if I understand it now

Wish you had answered me days ago.

What do you mean by "there's a net zero change in $\ce{H+}$ thus no buffering action took place"? The property of a buffer system IS to prevent drastic change in pH.
Buffer capacity, a measure of how much a buffer system can sustain a change in $\ce{[H+]}$ (aka. pH), (mostly) depends on two parameters -- the concentration of that buffer, and how close the desired pH is to its pKa. $\ce{H2CO3}$ has pKa's of 6.4 and 10.3. Given that the pH of blood is about 7.4 and better to stay that way, the base/acid pair, $\ce{[HCO3_^{-}]/[H2CO3]}$ (pKa=6.4) (plus a whole bunch of various proteins such as albumins in blood, all of which has its own pKa) does provide a good buffer capacity around that pH.
True, $\ce{CO2}$ is constantly removed through respiration, but it is also constantly generated by cellular respiration, making $\ce{H2CO3<=>CO2 + H2O}$ a "volatile equilibrium" and keeping both $\ce{HCO3_^{-}}$ and $\ce{H2CO3}$ in high enough concentration to sustain its buffer capacity.
HCl has a pKa of about -7 so it would make a good buffer around pH of -7. In an aqueous environment, all HCl molecules will 100% dissociate, and no $\ce{H+}$ will ever bind to $\ce{Cl-}$ because water itself will first "hijack" the proton as  $\ce{H3O+}$ (pKa=-1.74) before $\ce{Cl-}$ by about five order of magnitude.
---EDIT---
You may be thinking that when cells release $\ce{CO2}$ to the blood, $\ce{H2CO3}$ would be the first product, and in order for $\ce{H2CO3}$'s conjugate base to work as a base to absorb any extra $\ce{H+}$, first it must release a $\ce{H+}$, resulting in no net change in free $\ce{H+}$ and hence no capacity in balancing extra or insufficient $\ce{H+}$ to maintain the pH. Indeed, if $\ce{H2CO3}$ is the ONLY chemical species in the blood when it would not be a buffer. A buffer requires at least two species -- a potential proton donor and a potential proton acceptor, both of which in high and comparable concentration. pH is a measure of external free $\ce{H+}$, a result of final proton balance of all the acid and base in the blood, dictated by the Henderson–Hasselbalch equation. Thus when $\ce{H2CO3}$ is released in the blood, the blood's basic pH will causes most of $\ce{H2CO3}$ to become $\ce{HCO3_^{-}}$, releasing free proton. Again IF that's all the $\ce{HCO3_^{-}}$ in the blood after being made from $\ce{H2CO3}$, the blood's pH will drop, but there is already abundant amount of $\ce{HCO3_^{-}}$ in the blood, helping the system to reach new equilibrium. Of course, the buffer capacity of blood is not infinite. If there is so much metabolic acid being produced that it shifts the ratio of $\ce{[HCO3_^{-}]/[H2CO3]}$ toward excessive acid, acidosis would occur.

I'd hate to see what it takes to get water at pH of -7.

@user137 it need not be water.. It can be any solvent. Base/acid/salts etc are defined with respect to a solvent (which is water in most cases). If H₂SO₄ is the solvent then K₂SO₄ will be a base, not a salt. You can also imagine what if ammonia is the solvent.

What do you mean by "there's a net zero change in H+ thus no buffering action took place"? I mean that the H+ absorption is nice and all, but it's only made possible by producing a H+ at an earlier step. It's like saying glycolysis produces 4 ATP - it does of course but there's 2 ATP needed for glycolysis, so the net gain in ATP is only 2. I accepted your answer btw, thanks for the help (and commenters) but I'm not sure if I understand it any better now.

I think I have better understood your difficulty. You may be thinking that when cells release CO2 to the blood, H2CO3 would be the first product, and in order for H2CO3's conjugate base to work as a base to absorb any extra H+, first it must release a H+, resulting in no change in free H+ and hence no capacity in balancing extra or insufficient H+ to main the pH. Please see Edit.

I don't personally understand how you can discuss this buffering system without discussing the role of the kidneys.

Isn't that like saying 'glycolysis produces 4 ATP, we can ignore the 2 ATP that are needed for glycolysis because cells are bursting with ATP'? The net effect is +two ATP, like here it's +zero H+. Anyway thanks for the help I'll go back to review basic buffer/law of mass action and the role of the kidney in acid/base balance, I think that'll help. Sucks that I can't find a source that describes the big picture, everything I found so far separately describes all the systems (lungs, kidneys, red blood cells) involved without drawing a lot of connections with the others systems.

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Superpatients for Cancer resistance
I was reading an article on MIT Technology review about superpatients for low cholesterol that got me thinking whether such patients exist for cancer.
The article is
http://www.technologyreview.com/featuredstory/532421/the-search-for-exceptional-genomes/
I had also previously read an article on naked mole rats and the hyaluronan in the ECM.
http://www.wired.com/2013/06/naked-mole-rat-cancer/
Therefore, I am wondering whether there are any current studies, that is trying to discover the genetic outliers for cancers. Ie, humans that have hyaluronan in their ECM that is almost naked mole rat like. Since I understand that with a genetic pool of 7+ billion there has to be at least one outlier.
Thanks


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Can plants grow under extreme (>1%) carbon dioxide concentrations?
Related to but distinct from this question due to the concentrations involved.
While small carbon dioxide concentration increases can positively impact plant growth under some circumstances and at the same time negatively affect it under other circumstances, these changes are relatively small (doubling CO2 from 0.04% to 0.08%).
Is there any research on plants grown at extremely high (>1%) carbon dioxide concentrations in the air, assuming Earth atomspheric pressure? For the purpose of this question, assume that the plants are supplied with pH modifiers such as limestone in the soil to prevent soil acidification.

Yes they can, but their normal growth is somewhat impaired. A study by Bugbee and collaborators showed that while the yield of rice and wheat increases with CO2 up to about 0.1% CO2, yield decreases sharply as CO2 climbs from 0.1% to 0.25%. There is a smaller loss in yield as CO2 is further increased from 0.25% to 2%.
One interesting thing to note about the study is that the above results turn somewhat on how "yield" is defined. Bugbee defines yield in terms of the mass of the parts of the plant that people can actually eat. They make a note in the study that the vegetative growth of the plants (the green leafy parts humans can't eat) was not affected by the jump from optimal to super-optimal CO2 levels.


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Identifying a tree with an image
I have trouble identifying a tree that I saw on a vacation. This is the image:

I would like to know the name of the tree, I only know that its not European.

Where did you take this image?

I took it in southern france but I asked the owner about the tree and she said that its not from there.

but it still could be european

I think you should look into trees in the Rubiaceae family (which is very large with ~6500 species in total). Many species there have spherical inflorescences, and some are somewhat similar-looking to the ones in your picture, e.g. Neolamarckia cadamba or species in the Nauclea genus. This is however just a suggestion to guide you, and not a species determination. Note also that spherical inflorescences are relatively common in many plant taxa, so it might be found in another family than Rubiaceae.
This is what Nauclea orientalis (photo from Wikipedia) looks like, just to give you a sense of the basic similarity:

The individual flowers are however much smaller than the flowers in your picture.

@tly Very generous to "accept" my answer, but in fairness I don't think it is a full answer to your question.

floret color and density does not match with OP

@AlwaysConfused That is why I wrote: "..just a suggestion to guide you, and not a species determination". I'm suggesting a family, not a species.

I agree totally. this is why I put the comment there. Suggesting is good-thing, in fact our mind reach to a truth not in one-chance but in a long-chain of thought-experiments. I had just tried to tell the asker, that the mismatch is also high. I should use @tly before putting the comment.

The fruit strongly resembles immature lychee (Litchi chinensis). Since I have only seen the fruit, I cannot comment on whether the flower looks correct. The flowers appear to be slightly different from those in Wikipedia, especially in the number of "stamens"(?) per flower.

I don't think this is correct, since the picture in the question seems to show spherical inflorescences (clusters of small flower buds) and not fruits. The inflorescences to the right have started flowering. Lychee (and the related Rambutan) have spiked fruits, but these are not flower beds (rather the result of flowering).

@fileunderwater You're right, which is why I said that the flowers appear to be slightly different. I would consider this a partial answer, perhaps the actual plant would be phylogenetically related.

In what season was the picture taken?
Can you give an idea of the size of the objects present on the photo?
Based on the rough surface of the fruits, I would suggest having a look at Moraceae, and in particular at the Artocarpeae tribe within this family.


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Is there any conclusive study relating the food consumed and the occurrence of acne?
The internet says a million things about what to eat and what not to eat in regards to impacts on acne. For instance:

Refrain from dairy products.
Refrain from food heavy in unsaturated fat.
Refrain from too much sweet.
Consume fresh food (raw fruits & vegetables) but no cabbage and cauliflower.
No Alcohol
Etc.

My question is:
Is there really any relation between food consumed and the occurrence of acne?

The short and unsatisfying answer is no-- it remains controversial due to lack of high quality randomized clinical trials. According to an article in UptoDate, a reliable resource for many physicians, last updated September 2014, there is an association between acne and intake of milk in which milk components could exacerbate acne. Unfortunately, there have been no randomized clinical trials on this subject. According to the same article, "there is no reliable evidence that ingestion of chocolate is associated with an increased prevalence or severity of acne." In a similar light, the article continues on to say that "data on favorable effects of dietary factors such as zinc, omega-3 fatty acids, antioxidants, vitamin A, and dietary fiber on acne vulgaris are limited. Further studies are necessary to determine the roles of these supplements in acne vulgaris."
Reference:

http://www.uptodate.com/contents/pathogenesis-clinical-manifestations-and-diagnosis-of-acne-vulgaris?source=search_result&search=acne+and+food&selectedTitle=1%7E150#H8


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Cloning and Telomeres
I read that the length of telomeres in Dolly was shorter, because the DNA was taken from an old sheep. Shorter telomeres may lead to early aging. What is happening now with cloning? Do we use a telomerase to restore the length in a donor cell?

No, it doesn't seem to be common practice. A telomerase treatment would probably do more harm than good, and may be completely unnecessary in the first place.
Betts and coworkers published a study in which they examined telomere length in cloned cattle. They found that while telomere length in cloned embryos does start out somewhat shorter than in naturally produced embryos, by the time that the normal processes of embryonic development were in full swing telomere length in cloned and natural embryos was equivalent.
Betts' results make sense in light of the fact that telomerase activity (and the activity of many, many related proteins) is normally upregulated in embryonic cells.
As for Dolly, while it is true that her telomeres were shorter than those of an average age-matched sheep at the time of her death, it's far from clear that those short telomeres had anything to do with her decline. Also keep in mind that she didn't just keel over suddenly in the night, she was euthanized. A subsequent autopsy showed that she had a form of lung cancer caused by a retrovirus common in sheep.
Edit: why were Dolly's telomeres shortened?
This is a good question, as the findings of shortened telomeres in Dolly's case do contradict the findings in the Betts paper. Clearly we need more citations:
-"Analysis of telomere lengths in cloned sheep." Shiels et al, 1999
This is the original citation for the claim that Dolly's telomeres were shortened. There isn't too much extra information to be had as it's a very short paper (1 page letter). They did look at other cloned sheep created from types of cells other than skin cells (as Dolly was) and saw the same kind of telomere shortening relative to controls. They also make a point of mentioning that Dolly's telomere length may be within the normal variation for sheep.
-"Remarkable differences in telomere lengths among cloned cattle derived from different cell types." Miyashita et al, 2002
The investigators found that telomere length in cloned cattle was strongly dependent on the type of cell from which the clone was derived. For example, clones made from mammary cells tended to have shortened telomeres, whereas those derived from muscle cells had normal length telomeres.
-"The analysis of telomere length and telomerase activity in cloned pigs and cows.", Jeon, 2005
This group found that cloned cattle had normal length telomeres, whereas cloned pigs had elongated telomeres. By way of explaining these results, they found that telomerase activity was upregulated in cloned pigs relative to control pigs, whereas telomerase activity in cloned cattle matched that of control cattle.
How should we take all of this information? At the very least we can say that telomere length in clones is highly dependent on species and on source tissue, and that telomere length can increase, decrease, or stay the same in cloned animals relative to control animals. Clearly telomere length in cloned animals is a fiddly property. It is very likely that it also depends on the exact details of the cloning protocol as it was carried out (i.e. how much did the experimenter's hands shake when they inserted the needle to suck out the nucleus?, etc.).
So I would say not to read too much into Dolly's shortened telomeres. They may have been a result of her being a clone, or they may have been a result of natural variation. In either case the shortened telomeres were not linked to her ill-health, and it's likely that small tweaks to the cloning protocol would eliminate any telomere length discrepancies in future clones.

Somatic cells (used in SCNT) are also prone to recombinations and other somatic mutations.

@tel. Thank you for the answer. But then why Dolly had shorter telomeres, what was different?

@Barbos I posted an edit with some follow-up about Dolly's short telomeres. It's surprisingly involved!


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what's the vascular cambium?
is the vascular cambium equivalent to interfascular cambium or intrafascular cambium?
isn't the vascular cambium similar to the intrafascular cambium because both occur inside the vascular bundle

Welcome to Biology.SE. 1) You should chose a title that is much more specific. Don't be afraid if your title already states most of what you have to write in your post. 2) You should always limit your posts to only 1 question (I am not qualified to judge whether the fact that the current post contain two questions makes it too broad or not). 3) As the questions sounds like homework questions (although you tell those are not homework questions) you should tell us your thoughts and your attempt to answer the question. Knowing what you know and think make the answers much more helpful for the OP.

okay i will edit my post.


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What genetic distance model should be used when calculating genetic differences in Arelquin?
I'm using Arelquin to look at the genetic structure between a number of different populations. I  want to compare the populations by producing pairwise FST values, however I don't know what model for the genetic distances I should use.
The two models provided are Slatkin's distance or Reynold's distance. They both aim to linearize the FST values by transforming them [Slatkin's = FST/(1-FST), Reynold's = -ln(1-FST)].
How do I know if the FST values need to be transformed, and if they do need to be transformed, what model should I use?


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Why are canines not nauseated by similar foodstuffs/state of decay as human beings?
I am continually surprised at the items my pet dog is willing to ingest.
I understand part of the consumption is driven by nutritional instincts (licking salty liquids such as sweat) or nurturing instincts (eating baby faeces to prevent predators) but why does an animal with a sense of smell many thousands of times greater than our own not become nauseated by the same substances, smells or conditions that humans do?

Sweat
Faeces
Decayed foodstuffs
Assorted garbage
Untreated and/or dirty water

I have known my dog to bury a piece of rotting pork only to dig it up several months later for consumption.
In addition I watched dogs refuse to eat certain items (spicy meat etc) until their owner makes a move to take it back at which point the animal will swallow the item causing a gag, hacking couch or nasal clearance.
Is there a biological mechanism that suppresses the gag reflex in canines, is the need to consume overpowering their distaste or do they simply not find such substances unpalatable?

Your dog finds these things palatable, I assure you, and no gag-reflex suppression is needed.
I had a dog that would steal duck eggs from my flock, bury them all over the place, and dig them up when properly rotted to enjoy as a treat, and no, I'm not making this up. I saw her do it, ran across many buried duck eggs while gardening, and could immediately smell when she was enjoying one.
All that to say what smells good to a dog has nothing to do with what is acceptable to you. Many of your "dislikes" are conditioned: living in a society where cleanliness is valued and clean water is available, humans in such societies can afford to snub their noses at less sanitized things.
Manure may well elicit a completely different reaction to a farmer, who saves it carefully before spreading it on his fields to enrich the soil. To him, it might be the smell of a good crop next summer.
Many species exhibit corprophagia. It's not known why dogs (some, far from all) do this. Rabbits, for instance, eat their own feces after their first movement of the day. This is normal and nutritional for them.
Eating the feces of other species, particularly herbivores, is common among dogs and isn’t considered abnormal, just undesirable. My (same) dog followed my goats around like they were Pez dispensers. Since dogs can't digest cellulose, they get some of the advantage of eating plants this way.
Capybara, rabbits, hamsters and other related species do not have a complex ruminant digestive system. Instead they extract more nutrition from grass by giving their food a second pass through the gut. Soft fecal pellets of partially digested food are excreted and generally consumed immediately. Consuming these cecotropes is important for adequate nutritional intake of Vitamin B12. They also produce normal droppings, which are not eaten.
Young elephants, pandas, koalas, and hippos eat the feces of their mother to obtain the bacteria required to properly digest vegetation found on the savanna and in the jungle. When they are born, their intestines do not contain these bacteria (they are completely sterile). Without them, they would be unable to obtain any nutritional value from plants.
Eating garbage and human feces is thought to be one function of dogs during their early domestication, some 12,000 to 15,000 years ago. They served as our first waste management workers, helping to keep the areas around human settlements clean. A study of village dogs in Zimbabwe revealed that feces made up about 25% of the dogs’ overall diet, with human feces making up a large part of that percentage.
Coprophagia
Daily rhythms of food intake and feces reingestion in the degu, an herbivorous Chilean rodent: optimizing digestion through coprophagy
Coprophagia as seen in Thoroughbred Foals


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how to reconcile PDB structures' sequences via Uniprot references?
I’m trying to reconcile structures  in PDB entries with their  sequences as reported in their chemList.polymer.dbref entries.
E.g.: considering structures for HIV integrase:
PDB:3OS0 references UNP:P14350, focusing on integrase (len=391)
>sp|P14350|752-1143
CNTKKPNLDAELDQLLQGHYIKGYPKQYTYFLEDGKVKVSRPEGVKIIPPQSDRQKIVLQ…NRTVSIDNLKPTSHQNGTTNDTATMDHLEKNE
PDB:2B4J references UNP:P12497, focusing on integrase (len=287)
>sp|P12497|1148-1435
FLDGIDKAQEEHEKYHSNWRAMASDFNLPPVVAKEIVASCDKCQLKGEAMHGQVDCSPGI…LLWKGEGAVVIQDNSDIKVVPRRKAKIIRDYGKQMAGDDCVASRQDED
Why should these sequences be so different?!
and in case you think I'm focused on a bit of noise: there are 42 other HIV integrase structures all referencing UNP:P14350, and 43 other structures referencing UNP:12497 (and 79 others referencing UNP:Q76353, very similar to UNP:12497), 22 referencing an entirely different UNP:Q72498.

None of them is integrase:
P12497
Protein    Gag-Pol polyprotein
Gene       gag-pol
Organism   Human immunodeficiency virus type 1 group M subtype B (isolate NY5) (HIV-1)
P14350
Protein    Pro-Pol polyprotein
Gene       pol
Organism   Human spumaretrovirus (SFVcpz(hu)) (Human foamy virus)
Even if you meant the integrase product of the polyprotein, the second one is not even HIV.
From Wikipedia:

Human Foamy Virus (HFV) is a retrovirus and specifically belongs to
  the genera Spumavirus. The spumaviruses are complex and significantly
  different from the other six genera of retroviruses in several ways.
  The foamy viruses derive their name from the characteristic ‘foamy’
  appearance of the cytopathic effect (CPE) induced in the cells.[1]

good catch, @wysiwyg!  first, yes, i have been focusing on just the integrase bit of the polyprotein (eg, that's what the 1148-1435 BLAST qualifier does).  and  i've purposefly been including PFV in my analysis because "... PFV is very similar to HIV integrase and provides an excellent model for studies of retroviral integration".  but obviously i need to check organisms before aligning their sequences!  thanks again for your answer.


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Why didn't the polar bear change its color from white to black during evolution to absorb heat?
Polar bears are white in color and white color is not a good absorbant of heat. Why then didn't they evolve a black color to absorb more heat?

This is thought to be why they have black skin, and they have white fur because it is camouflage in the snow where they hunt, a black bear wouldn't be much good at sneaking up on a seal in the snow!

The white ones survived better and developed fur that would channel sunlight to the dark skin.

This question seems to assume that living beings have reached a pinnacle of evolution and that a pinnacle of evolution entails perfect adaptation, neither of which are true.

Additional nit:  "white...not a good absorber of heat" is untrue.  "White" implies uniform reflectivity in the visible spectrum (more or less), and there's plenty of energy to be had in other portions of the solar irradiance.

No seals ever surfaced near the ones with dark fur waiting for them at their air holes, so those bears died out, and only the “white” bears survived, since they were harder to see.

Polar bears do not have white fur - they don't have pigments in their fur hairs which makes them clear and translucent. The outer fur consists of hollow fibres, which shatter a part of the incoming light (the visible part) which makes them look white. This gives a very good camouflage in a white environment.
It was initially thought (see reference 1) that the hollow fibers work in the same way as fiber optic cables and direct the UV part of the light (the visible was thought to be shattered) towards the black skin of the bears where it generates heat, but this hypothesis has been disproved. The UV part of the light is simply absorbed by the bears outer fur and doesn't reach the skin (see reference 2 for details).
The hollow hair helps with the insulation of the skin and can change the color due to environmental influences. The tend to get yellow after feeding on seals due to the fatty substances from the animals. There have also been reports from zoos that algae lived inside the hollow part of the fur making the animals more grey and sometimes even green (see reference 3).
Reference:

Light collection and solar sensing through the polar bear pelt
Is polar bear hair fiber optic?
The greening of polar bears in zoos

Wouldn't IR, rather than UV, be the relevant part of the spectrum for being warmed?

UV has more energy. And how much IR is present in the arctis?

@Chris - The amount of energy in UV is utterly negligible compared to the bear's metabolism.  See for instance http://en.wikipedia.org/wiki/Ultraviolet_index (where you get numbers of under a watt per square meter even at noon in the tropics).  It might be useful for vitamin D production (if bears need it), but not for warmth.

@RexKerr That's probably why it plays no role.

Bears initially were dark. But in snow it is really poor camouflage, their victims will see them to early. So they evolved to white color.
They have a lot of fat and good fur to keep the temperature, they don't really need more sun energy. They need more food.
In the same way - in the forest all bears are dark - for camouflage.
Read here
http://www.polarbearsinternational.org/about-polar-bears/essentials/fur-and-skin

"in the forest all bears are dark" - What about panda bears?

Panda bears are the perfect color for sneaking up on bamboo.

How much energy could an Arctic-dwelling creature be expected to capture from sunlight?  I think not very much.  How much can it gain from having coloration that allows it to capture prey more easily?  Quite a bit.  Also, given the size of the polar bear, they will probably be generating more than enough waste heat from metabolic activity.  Indeed, if you do a little research, you might discover that the polar bear's problem is, indeed, getting rid of heat:

In bears, the basal metabolic rate varies with climate and season;
  Polar Bear has highest BMR.  Overheat easily when running; can't
  travel any great distance at speeds more than a walk.  Low
  surface-area to volume ratio favors heat retention. Tendency to
  overheat enhanced by layer of fat 11 cm (4.5in) thick.  Young cubs up
  to 6 months old, with little body fat, are susceptible to cold.   Use
  more than twice the predicted energy for moving at a given speed,
  perhaps due to bulky body.   Fat and fur both insulate.   As long as
  bear isn't exposed to wind, body temperature and metabolic rate remain
  normal at -37 degrees C (-35 degrees F).

From http://library.sandiegozoo.org/factsheets/polar_bear/polar.htm
Of course, even if the polar bear was a perfect absorber, it could get at most ~1kW/m^2 of energy from the sun, and that only on a clear day in the summer.  And that heat would be on the outside of its insulating fur & fat.
So there's the answer: a strong selective pressure towards white, little or none towards black.
Re waste heat: What is meant here is that when the polar bear (or any animal) consumes food, part of it goes to producing heat as an unavoidable byproduct of metabolism.  Larger animals usually have to get rid of excess heat, thanks to the surface/volume relationship mentioned in the comments.
For a reference, try thinking about this: http://en.wikipedia.org/wiki/Thermoregulation  And remember that not all answers are written down in a book (or web site, these days).  Sometimes you have to actually think and reason out your own answers :-)

Added: I think the problem with this question is the assumption that polar bears (or indeed, any boreal mammal) need to absorb heat.  Maybe that's down to anthropocentrism, since humans evolved from ancestors that lived in tropical climes, and so have adaptations (like sweating & nearly hairless skin) for cooling.  But if you read the links, you discover that more often the problem is getting rid of excess metabolic heat, and most boreal mammals seem quite comfortable in what we primates consider cold.  (I write this after coming in from playing with my two dogs, who love to run around in the fresh snow.)
You might also think about why almost all (non-domesticated) mammals have evolved protective or camouflaging coloration.  (The only exception I can think of offhand is the skunk.)  Indeed, a number of boreal mammals have evolved seasonal color changes (e.g. http://srel.uga.edu/outreach/ecoviews/ecoview130106.htm ), having darker summer colors (like their more southerly relatives), but turning white in winter.  That suggests that the benefits of camouflage strongly outweigh any possible benefit from solar heat gain.

The point of energy waste isn't true. Bigger animals have a smaller surface in relationship to their volume.

Oh, and can you please add references to you answer?

This is a false answer.

False how, exactly?

In addition to camouflage, consider that during the colder parts of the year, when they need the heat the most, the nights are longer than the day.
Darker fur would radiate more heat away from the body than the lighter fur.
So it's possible that they did evolve the white fur for heat - but in their environment, the coldest part of the year heat retention is more critical than heat gathering, and this would bias towards white fur, not black.

Why should darker fur radiate more heat? This is a question of the insulation through the deeper fur layers and the fat.

@Chris, this is basic physics: dark colors radiate heat more efficiently than light colors.

@Mark Only when there is heat to radiate. When the bear is insulated good enough (which they are) there is nothing which radiates of. In fact it is practically impossible to spot polar bears with a thermal camera. Additionally, dark fur would absorp light more easily than light fur.

@Chris I'm suggesting that one of the reasons there is so little emissions is due, in part, to the fur not being dark. It sounds like you are arguing that even if their fur were dark they would still not have heat emissions. Of course the fur only plays a part of the role in insulating the bear, but it still plays a part.

Although black is a better absorber of (heat) radiation, it is also a better emitter too. As Polar bears live in a cold environment, having black hair would cause them to radiate their body heat away more quickly. Their colour helps them to retain heat better - dark objects equilibrate to the temperature of their surrounding faster, lighter objects more slowly. If they were darker, they would require more food to survive.
Their black skin is irrelevant as the light has already been scattered/reflected away by the white/colourless hairs - as they look white, it's the reflected light that you are seeing.

It would be great if you could add some references to support your response!

interesting answer! Please add references and get some well-deserved credits here

Why then didn't they evolve a black color to absorb more heat?

This assumes that evolution is an active process, working by organisms' will or need.
Do not forget that the theory of evolution works from generation to generation, by random (imperfect and chaotic) mutations, most of which are unfavorable.
The polar bears did not evolve a black color because they can't decide that. If you believe in evolution, and you believe that a black color would draw more heat, increasing the animal's chances of survival over its white peers (so much that the white peers would eventually die off), then we are simply waiting for the black color to come around. Evolution is never finished.

This is a brief expansion on DrAlchemist's response; one that I intended to make myself, but saw that s/he had already covered the basics.
To see that black is a better emitter of heat we have to leave biology and go to physics, specifically quantum mechanics, even more specifically black body radiation. Like most things, absorption and radiation are equally balanced when it comes to a given material/color. A white object is slow to absorb heat and a black object is quick to absorb heat, as we have likely all seen demonstrated in elementary school. What my teacher (and likely yours) did not mention is that the white object cools slowly when taken out of the sun, but the black object will cool much more quickly. Black heats up quickly, and radiates just as quickly when the temperature differential inverts.
As a mental exercise, consider an idealized object that absorbs electromagnetic energy perfectly, called a black body. Turn a heat lamp on it, and it will absorb all the heat it receives. Turn the lamp off and, as in the argument above, it will become a perfect emitter of the radiation it absorbed.

This does not provide an answer to the question.

@Chris I think it does provide an answer by hypothesizing that because polar bears are white, they lose less heat due to radiation. However, this is probably not true: First of all polar bears lose heat by convection, not radiation, since they do not live in a vacuum. Second, if this was true you would expect the fur to be black and the skin to be white, since it is the skin that is warm and not the hairs.

Minor quibble: radiation occurs whether in a vacuum or not. And all we care about is which color is on the outside; a white metal ball painted black is the same as a black metal ball. But I do agree that convection is by far the primary engine for heat loss in the bears' environment and absorption/radiation is negligible. Ultimately I think their color doesn't matter one bit when it comes to heat retention, particularity since they spend a fair amount of time swimming in the Arctic ocean, a far better conductor of heat than even the frigid arctic wind. And yet they do not die of hypothermia.

I think an important point hasn't been mentioned yet.

Why then didn't they evolve a black color

The changes introduced by evolution initially are random.  Only the persistence of those changes over generations can be thought of in a "smart" way.
Technically, evolution can lead to some things getting worse!  For example, if mutations improve a creatures eye-sight but at the same time worsen it's hearing, both traits may end up surviving assuming the improved eye-sight makes more of a difference than the worsened hearing.

Well, Polar bears do have black skin; But, living in the harsh arctic conditions they've adapted several traits such as thick layer of blubber, wide paws etc. But their most peculiar trait is having a white fur coat; unlike other bears, polar bears have evolved to have white fur with hollow hairs which easily allows their black skin to absorb the radiations from the sun. So there's no problem with the heat intake.
Now, the reason behind their white fur lies in their quest to food. The white fur enables them to easily hide/blanket in their surrounding (the white masses of snow) i.e. it helps them in camouflage.
And, I guess that's it! Thanks!

Welcome to bioSE. Can you add some references to your answer?

The claim with the light absorption has eben dismissed. See the reference in my answer.


text:
Blood cells penetration
Is there a type of blood cell that can reach all other body cells? By "reach", I mean to "touch" the surface of the target cell.
If we look at the red blood cell for example, that moves in blood vessels, there are cells close by - after the wall of blood vessel - that get oxygen by diffusion and not by direct contact, as far as I know.

Drugs are usually not recognized by the immune system. Can you explain further, why you want to do this? And which disease you want to target?

Usually but there are some that may lead to immune response: http://en.wikipedia.org/wiki/Idiosyncratic_drug_reaction Also it is a way to improve targeting, theoretically. I added a link in the question about using of Red blood cells. My question more about the type of cells that can reach all the cells and organs in a body. Thank you.

That's why I was asking what disease you want to target. You not only have to get the drug inside you transporter cell, you have also get it out again on the right place (and presumably only there).

You right, Chris, it's very theoretical. There are no some special disease. I was thinking about using cell like "inside doctor". The cell will recognize the target and make some action. So need to chose some cell to start from it. This cell need to reach  all the cells in the body and about that is my question. How to teach the cell to do it, is much much complicated =) Just wondering if there is cell that reach all the places in the body (or most of them).

Why not use a PEGylated liposome or something to coat the drugs in a protective layer? You could add a targeting ligand to the surface to help direct it toward receptors at the target site and not need to rely on getting into and out of transport cells. Also, there is quite a bit of existing research to build on.

thanks you, but I just want to know  if there is some type of cells that can reach all the places in the body (or most of them).

Basically all circulating blood cells have approximately the same chance of reaching a target tissue. That's what blood is for, to release oxygen and nutrients to every cell in the body, and to pick up waste products. If plain old blood were unable to do this, the tissue would die. That's called ischemia. Sure, cytotoxic T cells have access to all the cells, but don't act independently of other immune processes. But you can choose other cells as well.

I don't thinks that it is true. For example Cancer cells don't get enough oxygen because red blood cells don't reach them, there is no blood vessels near them. So all the oxygen that they get is from diffusion through neighboring cells.

That's outright nonsense, and it doesn't belong here or anywhere else. If what you said was true, cancer cells would die and we wouldn't have to worry about cancer at all. Instead of guessing, why don't you do some actual reading? You can start with your own error. Here's a clue: Molecular mechanisms of tumor vascularization.

The amount of mitochondria in cancer cells is often very little. It's true that they create a blood vessel in the end. But there are stages that the main source of energy is  pyruvate - lactate. But again. That not what I am asking. As far as i know - red blood cells not touch all the cells in the body. They move mainly in blood vessel and not between the cells.

No, there is not. Cells in the bloodstream reach most areas in the body, but there are certain privileged areas which stop cells, drugs and macromolecules from leaving the bloodstream and entering the tissue. These privileged areas are thought to exist in sensitive or important areas for their own protection:

Immune privilege is thought to be an evolutionary adaptation to protect vital structures from the potentially damaging effects of an inflammatory immune response. (Wikipedia)

The most common example of such an area is the blood-brain barrier, but there other barriers to privileged areas, including the blood–testis barrier, the blood-retinal barrier and the blood-ocular barrier. Cells do not pass from the blood through these barriers, except in disease (Larochelle et al. 2011).

Related reading:
The first chapter of Blood Groups and Red Cell Antigens has a decent high-level overview of different types of blood cells and their roles in the bloodstream and the immune system.
How do immune cells overcome the blood–brain barrier in multiple sclerosis? Larochelle et al. 2011

Thank you! But in wiki - "Antigens from immune privileged regions have been found to interact with T cells in an unusual way" - that mean that T cells reach the region, just don't work.

That actually means that antigens that escape from the privileged regions (usually due to injury or illness) are recognized by the immune system in ways we don't understand. This interaction is not a normal occurrence. Reading further, you can see that there are immune cells in some of those areas (i.e. eye), they just don't move back and forth


text:
Phylogenetics and the Tree of Life
As far as I understand, evolution is nowadays pretty much analyzed through phylogenetic trees, that is cladograms. These are constructed using the available records and taking some key structures and deduce whether species acquired or lost it, thereby generating a node. By  this approach, chronology is of utmost importance, but chronological time is not. Hence, cladograms are not 'Darwinian' evolutionary trees as the latter are based on chronological time.
However, I cannot help myself when analyzing a cladogram and interpreting the accumulation of various nodes along a branch as moving through time. Isn't evolution all about time? At the risk of pitfalling myself into a 'this is a primarily opinion based question':
Isn't it just so that along a certain branch, each successive node has taken time to develop? Would it not be plausible to determine and assign a certain 'standard evolutionary time unit (a SETU if you like) representing the average time it takes for any organism to loose or acquire a certain trait, thereby allowing each node to be interpreted as time? Of course, the SETU would be a gross estimate, but could still potentially re-animate the Darwinian look on modern-day evolution.

Let's start with a short comment. You say [..]evolution is nowadays pretty much analyzed through phylogenetic trees[..]. Many evolutionary biologist make extensive use of phylogenetic methods but a good part of evolutionary biologist (most of them I would say) do not work directly with phylogenetic methods.

I am not sure I understand your question but I hope the following may help you either to understand the issue or to edit your question. Note that I am NOT a phylogeneticist (not sure this word exist).
What is the definition of "Node" in Phylogenetics
I think your definition of a node might be unusual. In phylogeny, a node is the most recent common ancestor shared by two sister lineages.
Time in a phylogenetic tree
Also, when you look at a phylogenetic tree, the axis along which lineages diversify represent the time (real time in years). Now, we use different methods in order to make estimation of this real time such as the rate of neutral substitutions. You may want to read about molecular clock

each successive node has taken time to develop?

I am not sure what you mean by "develop" here. Develop usually means the process by which a given individual/organism change phenotypically through its lifetime. See Developmental Biology.

average time it takes for any organism to loose or acquire a certain trait

Again, I am not sure whether you talk about development or evolution here as you talk about "any organism" and not about "any population". In any case, an average time for a population to acquire a given arbitrary trait is a concept that 1) is valid only for discrete trait, 2) that is very dependent on the kind of trait you want to consider, 3) that will varies a lot from one given trait to another and 4) is extremely dependent on when you consider being the starting point of the evolutionary process toward the creation of the given trait. Therefore, it doesn't makes much sense.
Currently used "standard evolutionary time unit"
However, you can use similar concept for quantitative traits. The Darwin (d) is a unit of evolutionary change (invented by Haldane and named after C. Darwin). It is defined as the e-fold (e≈2.7) in a mean of individual's trait in a population over million of years.
Similarly, the Haldane is a unit of evolutionary change (I don't know who invented it and it is obviously named after JBS Haldane) and correspond to the number of standard deviation (of the distribution of individual trait in the population) change in the mean of individuals trait in a population per generation. The Haldane unit is therefore dependent on the selection pressure, the additive and non-additive genetic variance and environmental variance (therefore the heritability) and the mutational pressures.

...phylogeneticist (not sure this word exist). I'm going to say that it does, and just means someone who practices phylogenetics. A better word might be taxonomist.

Thanks tel for you approval! Chris, let us know whether the answer(s) address your question and answer it.

This is definitely very helpful. And it pretty much answers my question(s) as to how I should/can interpret cladograms, their frequency of use, and the meaning of 'time' in a cladogram. Cladograms are very abstract, but very helpful and this answer clarifies a lot about them. I must say that my perception of a 'node' was likely incorrect and I could re-phrase my question to make it more appropriate, but your answer is great and I leave my question as is, if that is OK with everyone :)

Something like what you describe does exist, and is called a molecular clock. The rate of change in certain genes and non-coding sequences has been correlated to other evidence (fossil record, etc.) in such a way as to allow you to estimate in absolute terms how long a given set of mutations would take to occur naturally.
Keep in mind that only certain genes have the required property of accumulating mutations at a more or less constant rate with respect to time. Most genes accumulate mutations in a more stochastic fashion.


text:
What is an operon?
What is an operon in a eukaryotic cell, and how does it regulate the expression of genes? I've already read Wikipedia, but it is not enough clear to me. Unfortunately my knowledge in genetics are very poor!

You could check out the Encyclopedia Britannica.

There are some naturally occurring polycistronic mRNAs in flies and worms. You can also make artificial polycistronic DNA using IRES sites or self-cleaving 2A peptide sequences (which were isolated from viruses). Which one are you asking?

Is an operon just several genes with the same regulation, so they are transcribed at the same time? In prokaryotes the genes in an operon are often placed next to each other so they can be transcribed as one mRNA and take advantage of their ability to translate polycistronic mRNA, but in eukaryotes where polycistronic mRNAs are less common, they might not need to be near each other in the genome.

@Superbest: I'm asking about naturally occurring polycistronic mRNAs

Operons were once thought to appear only in prokaryotes (and viruses of prokaryotes), but there are now known to be a number examples in eukaryotic organisms. These are mostly seen in nematodes and insects.
Generally an operon is a functional DNA unit which contains a cluster of genes which are regulated by one promoter/repressor element and which are transcribed together. These are genes which functionally work together in a close context. A good example for this is the lac operon in bacteria.
In prokaryotes the expression of the operon leads to polycistronic (multiple open reading frames on the same transcript) mRNA, which is then translated into proteins.
Operons in eukaryotes are also gene clusters (often of functional closely related proteins), which are regulated by one regulatory unit (promoter). See figure 1 from reference 1:

There are different ways of mRNA arising from this phenomenon. First the mRNA can be dicistronic and most likely has internal ribosome entry sites (IRES) which allows the initiation (or re-initiation) of the translation of the second gene. Another possibility is the cleavage of the primary mRNA strand into two (or more) monocistronic mRNAs. And finally it is also possible that the dicistronic transcript is alternatively spliced to get different (monocistronic) mRNAs.
If you are interested in the details of eukaryotic operons, I strongly recommend reading at least the first reference (and probably also following up some of the related citations (on the right on the NIH website)).
References:

Blumenthal, T. (2004). Operons in eukaryotes. Briefings in Functional Genomics, 3(3), 199-211.
Pi, H., Lee, L. W., & Lo, S. J. (2009). New insights into polycistronic transcripts in eukaryotes. Chang Gung Med. J, 32, 494-498.

One of the best examples for eukaryotic operonic RNAs can be miRNAs produced from clusters. They arise from same primary transcript.

Since the OP specifically asks about eukaryotic operons, and appears to be understand prokaryotic ones, is it possible to at least also include a diagram of a eukaryotic one? The fly Adh/Adhr paper has a simple figure, but I haven't had time to read it very thoroughly.

+1 for using c elegans and drosophila examples in your answer


text:
Why is mRNA needed in the Protein translation?
The original question was to predict the basic requirements for information storage. Then the discussion moved to why is it necessary to include mRNA in the protein translation process. Why can't there be a similar chemical molecule like tRNA which can directly read from DNA and exclude the mRNA intermediate. Also is the current translation process optimal in the sense that can there be a system which does not need mRNA or a similar intermediate altogether. Or is the presence of an intermediate a necessary requirement.

Although this does not directly answer the question, I think you could take the inverse point of view and rather ask why/when is DNA needed for the replication of an organism.

One reason is that an intermediate like mRNA allows for higher amounts of protein expression. You can have multiple mRNA molecules that are translated simultaneously. If you read directly from DNA you can have at most two translations in parallel.
I'm not sure about this, but I would imagine that having to unwind the DNA double strand every time for translation could be a drawback to directly reading from DNA as well. The mRNA is also subject to various forms of regulation, which might be an advantage as well for the added intermediary.

Beat me by 15 seconds because I thought I could find more references.

"If you read directly from DNA you can have at most two translations in parallel." - upvoted, but this is not true, you can have many parallel translation in series right after each other in one or many codon distance - depending on the space necessary between them. I think a more accurate explanation, that accessibility would limit the translation speed.

Is there data on how fast translation and transcription happen? If translation is slower than transcription (which it might be due to the larger tRNAs diffusing more slowly, having 20 amino acids vs 4 nucleotides, etc), then there would probably be an advantage to quickly transcribe the mRNA from DNA, then pass the mRNA on to ribosomes for the slower translation. Might still be able to do multiple transcriptions at once like inf3rno mentions.

@inf3rno I was thinking about including the fact that multiple ribosomes can read the same mRNA at the same time, but decided to skip that to avoid making it more complicated than necessary. And one codon distance is certainly not possible, the ribosome is quite large.

@user137 you can perform many translations from a single mRNA. So you don't need to transcribe the DNA into mRNA as often as you translate the mRNA into protein.

@MadScientist Right, but there might still be a speed difference between the two, and I suspect translation is the slower one, even if it doesn't need to be. I might be wrong, transcribing a gene of length N needs N ribonucleotides, while translating that mRNA only needs at most N/3 amino acids (splicing out introns would reduce the length, untranslated regions don't need amino acids, etc) so that the reduced material cost compensates for slower speed.

I don't have a lot of references for this, but it's too long for a comment.
Separating the roles of RNA and DNA helps to better control protein production and gene replication. If ribosomes worked directly on DNA, it would probably be very hard to replicate that DNA, as the DNA polymerases would collide with the ribosomes. You'd have to stop protein production and move the ribosomes out of the way before you could copy the DNA. Keeping mRNA separate allows the ribosomes to keep making protein while the DNA is being replicated.
However, transcription of DNA would be similar, where the DNA replication could collide with the transcription machinery. I can't find anything about that situation so I don't know how its regulated or how often it happens.
Additionally, having mRNA allows amplification and further regulation. Every mRNA copy can make several protein copies, so the amount of protein produced from a single round of transcription can be higher than if the DNA were read directly by a ribosome. mRNA also has many binding sites for miRNA and other regulatory RNAs. If DNA were read directly, that wouldn't be possible.
There are also some cases where mRNA is stored and used later, such as immediately after fertilization, or in platelets and erythrocytes where translation can happen even after transcription stops due to loss of the nucleus.

In lay man terms you need your DNA to remain intact and protected. so instead of shipping it to the cytoplasm where a lot can happen to it, the cell makes an intermediate mRNA. if anything does wrong with mRNA, the cell can discard it and make another copy and after translation the copy of mRNA is also discarded.You also have the amplification; instead of making one protein from one gene on a DNA strand, and then one more and the another, we can just make a bunch of copies of mRNA and send them to the nucleus where we can make as many proteins as we need. by doing this there is minimal manipulation of the original DNA strand and the cell get a lot of product over a short period.

"instead of shipping it to the cytoplasm where a lot can happen to it"..... Doesn't apply in case of prokaryotes

yes thanks for that i was mainly focusing on eukaryotes


text:
Is there a risk of localised die-off when plants bud too early?
I've been taking a few walks in the countryside in Scotland and England this winter (end of December 2014). Some parts of England haven't had any frosts yet, which is very unusual, and it's been generally quite warm since summer ended.
My friends and I agree that there's quite a lot of stuff putting out shoots and buds, as if it's April already. I can imagine that this means a lot of small fragile plants could get killed if a hard frost comes in the next few weeks. If so, it seems natural to expect that next summer will be marked by an absence of these plants, and, being dead, they won't put out seeds or otherwise reproduce for next year. In other words, we're expecting some species to experience localised die-off.
Is this plausible or are we just imagining it? If it's actually happening, is it something to actually be worried about? i.e. will a large portion of the seeds/shoots/buds/whatever refrain from growing even if some are being tricked by the mild winter, or will they be cold-resistant if they're coming up now, or is some other mechanism going to make it all okay? Alternatively, is this winter likely to trigger a large ecological change?
I realise this question doesn't single-out any particular species for attention, and perhaps it's too much of an open question for StackExchange's taste, but I'd very much appreciate some insight into how fragile or robust is the distribution of British plant life when the weather is abnormal, as it is right now.

If you're talking about shoots or buds coming out of individual seeds, then those plants are probably doomed. Most seeds are "designed" as one-shot delivery packages. In this case, they'll bud, be killed off by a frost at some point during the winter, and then be spent.
For a perennial plant like a tree that buds year after year, the impact of an early blooming will depend on the species. As per a Q&A from Cornell (Will Warm Winter Wither Plants?, 2007), most plants growing in a temperate climate (like that of Britain) will have experienced warm winters before and will have at least some evolutionary adaptations to help them deal with occasional aberrant weather. For example, even if you do see some fresh buds on a tree this time of year it is likely that the majority of its bud primordia (the parts of the plant that will someday become buds) have not developed. Although you won't see regrowth in the spring of most of the buds that opened early, you will see normal development of the buds that stayed dormant during the winter.
As for the question of wider ecological change, one anomalous year isn't going to make a difference because, as you say, a large portion of the seeds/shoots/buds/whatever refrain from growing even if some are being tricked by the mild winter. However, if a string of mild winters cause significant die-off year after year you would start to see changes in the ecosystem. It works the same way for many with loosing their hair...


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Besides hemoglobin, what proteins are present in red blood cells?
I knew that mature red blood cells (RBCs) lacked nuclei, but I wasn't aware until just now that they also lacked ribosomes and mitochondria. Most cells in the human body all contain a common laundry list of housekeeping proteins and RNAs (including mitochondrial proteins and ribosomal RNAs), but I guess RBCs lack a number of them. Do they still have all of the other organelles? Obviously hemoglobin (and to a lesser extent carbonic anhydrase) makes up a large portion of the dry weight of RBCs, but are other proteins still present? If so, what are their relative abundances?
For example, do red blood cells have any of the normal metabolic (i.e. ATP producing) proteins? Obviously they don't have any of the TCA cycle proteins, but do they still have the glycolysis ones?

Afaik they use mostly glycolysis to produce energy, so proteins of that pathway must be there...

Reticulocyte stage is when the ribosomes are still present and after that no new protein synthesis occurs. However RBCs have a lot of proteins and major proteins other than haemoglobin are cytoskeletal proteins and ion channels/pumps (In fact, cytoskeletal proteins are more abundant than haemoglobin). It is the Na+-K+-ATPase that consumes most ATP. As you correctly identified the RBCs produce ATP via glycolysis and glycolytic enzymes are also present. Note that deficiency of pyruvate kinase leads to haemolytic anaemia.
For a detail on the proteins present in human RBSs, see this paper. They have studied the RBC proteome by ion-trap MS. The top 5 proteins (from Table-1) are:
No.    Protein description              Molecular mass (Da)    Gi Number    Sequence     No. of identified
                                                                           coverage(%)      peptides
1      Spectrin α chain, erythrocyte         279,916.5          1174412       48.0           77*
2      Spectrin β chain, erythrocyte         246,468.1          17476989      48.0           76*
3      Ankyrin 1, splice form 2              206,067.9          105337        45.0           55
4      Ankyrin 1, isoform 4, erythrocytic    203,416.6          10947036      45.0           50
5      Ankyrin 1, isoform 2, erythrocytic    189,011.2          10947042      46.0           48
Although in this table you cannot find glycolytic enzymes other than GAPDH and Aldolase, but other enzymes are also present. They are perhaps not detected in this experiment because of overwhelming levels of structural proteins. You can check this old paper that shows a study of different glycolytic enzymes from erythrocytes. It is also to be noted that the glycolytic pathway flux is not as smooth as in other cells. So some accumulated metabolites are probably exported out of the cells to keep the flux smooth[ref Full text not found].


text:
Has any research lab done serious work to engineer new bacteria which assemble graphene wafers?
I was thinking about crazy uses for engineered bacteria. Nano-assembly of Graphene seems like a potentially excellent target for the technology. Have any research/full-blown labs worked on this? Any papers on it?
What would be some of the difficulties?

Surprisingly, the answer is yes. In 2012 Tanizawa et al published a paper titled Microorganism mediated synthesis of reduced graphene oxide films. The gist of it is that most of the steps (including the structuring of the graphene sheet) were carried out with chemical synthesis, but a final reduction step from graphene oxide to graphene was carried out using bacteria from a local river.
Probably not quite what you were thinking of, but I imagine this is the closest you'll get for right now.

cool... as I am interested in nanotech, this is very impressive...+1


text:
Concentration of degenerate primers should you dilute to?
I'm a little embarrassed to ask but when you have for example four degenerate primers and the end protocol says that the final primer concentration should be 10 µM working stock, should you make the primers 10µM total (2.5 µM each) or 10 µM for each degenerate primer?

You can just add 2µl from each working stock (10µM) to your PCR mix of 20µl.
You can check this protocol.
Caution: The author has used $l$ instead of $\mu l$
He uses 5µl of each primer (20µM) in a 50µl reaction. This is double of what I mentioned. IMO it is best to try with a lower concentration and then increase it if necessary. Excess primer concentration can give rise to some nonspecific binding and amplification if the primers are not perfectly designed.
From this site:

Using degenerate primers
Because a degenerate primer is really a mix of different primers, only
  a fraction of the degenerate 'primer' will actually work in the PCR.
  One would therefore need to increase the primer concentration in PCR,
  sequencing reactions, etc. If a primer is 8-fold degenerate, the
  concentration should be raised 4-8-fold, and so on. However, for
  higher degeneracies, e.g., 64-fold, one cannot increase the primer
  concentration 64-fold and would have to try their luck with a
  5-10-fold increase only.


text:
Are there known examples where an evolved mechanism "echoes" one originally provided by the environment?
Short summary
I am a researcher in origins of life, a field that deals with hypotheses about evolutionary processes that took place before LUCA (the last universal common ancestor), and with the chemical processes that gave rise to life and evolution in the first place. This is very hard to study empirically, and as a consequence there are many competing hypotheses. However, I've noticed that many of them have a common form, which I will describe below. My question is about whether hypotheses of this particular form exist (and have been investigated, for example using phylogenetic methods) in post-LUCA evolutionary biology.
My reason for asking is that my colleagues and I were not able to think of a good example. If no example is known in post-LUCA evolutionary biology then it casts doubt on the plausibility of this type of hypothesis in pre-LUCA evolution. I suspect this is the case, and therefore my ideal answer would provide me with bibliographic material to support a claim that there just aren't any good examples of this in evolutionary biology. However, I would also be happy to be proven wrong with a really good example.
Longer explanation
Hypotheses regarding the origins of life are difficult to test empirically, because phylogenetic methods can give us little direct evidence about anything before LUCA, and because there are no fossils dating from that time. (The entirety of Earth's surface has since been replaced by plate tectonics.) Consequently there are a number of competing hypotheses that differ from one another in almost every way. However, I've noticed that many of them have a common form: they say that

one or more of the features of a modern (i.e. post-LUCA) cell were originally provided by an external mechanism, in the form of abiotic chemical processes that took place in some very specific microenvironment, and
evolution eventually provided a solution that very closely echoed the one that had originally been provided by the environment.

Point (1) seems relatively easy to satisfy in an evolutionary scenario; it's point (2) that I'm specifically interested in. The two most popular hypotheses in the field both have this form:

Some forms of the The RNA-World hypothesis hold that originally, RNA nucleotides were produced by purely chemical processes in the environment, and that life evolved from self-replicating RNA molecules made up from these abiotically-produced monomers. Later, life evolved a cellular metabolism by which it could construct its own RNA monomers. This satisfies point (2) because it says that the environment provided RNA rather than some other heteropolymer with catalytic properties; the evolutionary solution echoes the environmental one in that it uses the same complex molecule.
Wächterschäuser's Iron-Sulphur World theory, and many of its descendants, including Russel's alkaline vent theory, hold that the reductive tricarbolic acid cycle (rTCA cycle, aka reverse citric acid cycle) was originally catalysed by mineral surfaces. This enabled the formation of the first cells, which eventually evolved enzymes that could be used to catalyse the rTCA cycle without the mineral catalysts. This satisfies point (2) because it says that the first evolved solution used essentially the same chemical pathway as the one provided by the environment, just with different catalysts.

(Not all hypotheses in origins of life have this form. Some versions of the RNA World theory hold that RNA-based life was preceded by life based on some other heteropolymer, for example. But the hypotheses described above are very popular.)
From an evolutionary biology point of view, point (2) seems rather an odd feature for a hypothesis to have. Evolution is great at producing novel solutions to problems, but to my knowledge it isn't good at copying old ones. (Mimicry doesn't provide a counterexample to this, since it's about appearance rather than mechanism, and often the mimic produces the same visual effect through a very different mechanism. For example, although the treehopper Cyphonia clavata mimics the outward appearance of an ant, it does so not by being anatomically similar to an ant but by having a face on its butt.)
Consequently I'm looking for known examples from evolutionary biology that satisfy both point (1) and point (2). That is, I'm looking for examples where a species originally relied on some relatively complex process in its environment, and became less dependent on its environment by evolving a mechanism that closely echoes the one originally provided by the environment.
An example that might fit the bill would be a species that was originally unable to produce a key metabolite (e.g. an amino acid), but then later evolved the ability to produce the metabolite for itself. Evidence for this might be constituted by finding a species that produces the metabolite using a novel set of proteins, indicating that the capability to produce the metabolite was lost and then re-evolved. It would make an even better example if the novel proteins catalyse substantially the same chemical pathway that other species use to produce the same metabolite.
It may be that no good examples of this exist, which is actually better for me than if they do. More than any particular example, the main thing I want to know is whether ideas along these lines have been discussed in evolutionary biology at all (perhaps outside the context of the origins of life), and if so where I can find the literature on it.

If cold blooded animals get their heat from the environment, then warm blooded animals might be described as evolving to provide their own heat.

You should narrow this question down to a specific topic. It seems too broad to me.

I don't think the question is too broad, however after reading @user137's comment I would tend to think that maybe, the question is not very well defined. What do you think Nathaniel? Would endothermic (see here to understand this terminology) animals be an answer to your question?

Note the interesting but controversial examples of genetic assimilation

@WYSIWYG I can only imagine I've phrased the question poorly, as in asking for example of something very specific. If you can point me to particular parts of the text that can be interpreted as asking for something broad, I'll do my best to fix them.

@Remi.b I can't deny that endothermic animals are an example. However, they are a poor example for my purpose, because generating heat is quite an easy thing to do chemically, whereas the hypotheses for the origins of life require things as complicated as the TCA cycle to evolve this way. When I'm at a non mobile device I'll edit the question to put an emphasis on that.

@Nathaniel I don't think it is badly phrased. I just think that to list all possibilities would be a little difficult. You can narrow down to some specific environmental factors (like temperature; as discussed in previous comments)

@Remi.b genetic assimilation can't be used to draw a good analogy with the origins of life, because there was nowhere to assimilate genetic material from, so I'm telly looking for examples where the feature was evolved independently. (I'll also edit that in.)

@Remi.b On a different note. Is endothermic for warm-blooded a correct term? In the sense of reaction it means one that absorbs heat. Isn't homeotherms (and poikilotherms for ectothermic) a more appropriate term

@user137 your example is useful and appreciated. See my comment to Remi.b above.

@WYSIWYG I've done my best to narrow it down to something much more specific. (Re-reading it, it indeed seemed to be asking for something much more general that what I'd intended.) I've also made the edits referred to in my comments above.

@WYSIWYG endothermic is standard terminology. Endo means 'within', so I guess in biology it means something that makes heat within itself, whereas in chemistry it means something that needs heat within itself in order to happen. I agree it's annoying that it means the opposite thing in the two fields.

@Nathaniel Would a potential example be something like essential amino acids that an organism cannot make on its own, so it has to get them from the environment or food? So if that species somehow developed a method to produce that amino acid, then it wouldn't need to obtain it from the environment anymore. I'm not aware of any examples, just trying to figure out what you're looking for.

@user137 yes, if there's a known example of that it would make a very good example. (Of course I know that there are many known examples where a species has lost the ability to make an amino acid, but this is the point I eventually want to make - if the environment provides a species with something, there's no pressure for the species to evolve that thing for itself, and so it doesn't tend to happen.)

Interesting question, but I would imagine that it could be difficult to obtain evidence for this (even when it has occurred), since I would imagine that these kinds of features are rarely seen in fossils (especially along with knowledge that the feature was originally provided by the environment). And the time period we have been able to observe these kinds of processes directly is not very long from an evolutionary perspective.

It was getting long for a comment:

A species that was originally parasitic, but then evolved to survive     independently of its host by independently evolving the
  same       metabolic functions
A predator that originally relied on its prey to synthesise some vital metabolite, but later evolved the ability to produce the
  missing metabolite for itself through a similar pathway

A parasite is generally evolved from a free living form. It has a reduced genome and cannot synthesize many vital nutrients. It is unlikely that it would acquire a gene that would enable it to live freely. A parasite, in general does not require to synthesize nutrients; so it is not under any pressure to acquire that function as long as its host is surplus.
Same is in the case of predators.
Basically, in higher organisms it is difficult to conjure a new gene; it is a slow process and happens via gene modification. However, in lower (basically unicellular) organisms lateral gene transfers are much easier and it is possible that they can acquire new metabolic pathways from other organisms. Have a look at this article.
In lower eukaryotes endosymbiosis, is another way by which new metabolic pathways can be acquired relatively fast. A diatom called Rhopalodia gibba, which already had a red alga derived secondary plastid, acquired another cyanobacteria derived green plastid for nitrogen fixation. You can have a look at this post too.
For your question on independent acquisition of traits; almost all metabolic pathways are evolved like that only. Enzymes isoforms that can bind to a slightly different substrate gave rise to another step in the pathway.
It is also possible to engineer a new trait:
Nucleotide analogs have been created to make a 6-letter nucleotide system which can be replicated by PCR[1, 2]. Earlier this year this was demonstrated in-vivo[3]. It has been shown that these new nucleotides can also be transcribed (see cross references in [3]).

I'm very sorry for not making my question clear enough. I'm not just asking for examples of the evolution of metabolic pathways. I'm asking for examples (if they exist, which they may well not) of metabolic functions which at one time were provided by the environment but which are now performed by the organism using a similar molecular mechanism. It's not a particularly easy thing to make clear, but I will have a think about how to do it better.

@Nathaniel well, by pathway I meant that a newly acquired function plugs itself in the network an expands the pathways. But by endosymbiosis new networks can also be incorporated (thats what I meant there). But for your question I guess the answer is - almost every gene. Recent examples would include genes for drug metabolism.

You're answering a different question from the one I'm asking. As I said, this is my fault for not being clear enough, and I will have to think more about how to improve the question.

The E. coli long term evolution experiment showed that E. coli had evolved a function (the metabolism of citrate) which was not required in the ancestral environment, but which evolved naturally and was selected for in this new artificial environment. AFAIK, this is the only example of a function that has been observed naturally evolving under controlled conditions.
The reason we are unlikely to see any metazoans evolving new metabolic pathways is due to the fact that they have long lifespans and therefore reproduction times. However, as WYSIWYG has already mentioned, almost all metabolic pathways evolved that way, it is just hard to observe due to the long time spans involved.

I'm very sorry that I wasn't able to make my question clear. I'm not just asking for examples of the evolution of metabolic pathways. I'm asking for examples (if they exist, which they may well not) of metabolic functions which at one time were provided by the environment but which are now performed by the organism using a similar molecular mechanism. Examples would likely come from phylogenetics, rather than direct experimental observation.

See this more as a comment than an answer, since it became too long for a comment. However, I think some of the examples should be relevant to refine your question.

One thing that I find vague in this question is what exactly constitutes a "process"/"function"? To me, this can be almost anything. You seem to be focusing on molecular biology and biological pathways, but I think it is just as reasonable to think in terms of large scale processes. If so, there are lots of processes that seem valid in my mind, relating to e.g. reproduction and dispersal.
For instance, in primitive plants (and other taxa) fertilization is external and dependent on environmental moisture to transport gametes. Organisms with internal fertilization has bypassed this by providing their own mechanism for fertilization, which does not depend on environmental processes (to the same extent). The evolutionary forces behind this was maybe/probably that it was more efficient and allowed colonization of new environments.
Another similar example is seed dispersal in plants, where some are wind dispersed ("primitive" state) and others use active measures to eject seeds (ballochory). By doing this they have bypassed the dependence of wind to disperse their seeds. The same kinds of mechanisms can also be found in groups of mosses.
In both these cases a function that was previously external and environmentally mediated is now provided by the organisms themselves, and they involve quite complicated morphological and anatomical adaptations. Do you find them valid for your question? These are just two examples, but there are lots of similar cases.
More in the line of comments to your question, I think you should provide one or two references to the hypothesis you are referring to (i.e. where it has been used/discussed), which would make it easier to understand exactly what you are after (and also provide an entry into the literature). This could maybe also help explain why the "...evolved solution 'echoes' the one provided by the environment". At the moment I don't understand at all why this should be the case in general. Adaptive evolution happen because of selection that acts on differences in fitness, and it is indifferent to whether the mechanism echoes a previous solution to a similar problem (except for the fact that evolution is constrained by the evolutionary history of organisms).

Thank you for the answer. The examples are indeed relevant. I do intend to make the requested improvements to the question, including references, its just a little hard to find the time and enthusiasm at the moment. I also don't understand why evolved solutions should echo those provided by the environment, yet hypotheses of this form are common in the origins of life, hence the question. (I hope my future edits will make it clearer what I mean by that.)

(Though I guess your examples are somewhat lacking in the "echoing the environment" property, because the 'complicated anatomical mechanisms' they use don't resemble the original environmental mechanism. I do need to clarify what I mean by that, and I hope to find the time today or this week.)

I've re-written the question, and I hope it's clearer now.

@Nathaniel I think the questions was greatly improved by the rewrite. The "echoing" aspects are also more clear, since the examples you've provided indicates the reason why this might occur. In both your examples, it is plausible that the primitive "organisms" have evolved other pathways/features that depend entirely on the function in question (RNA & rTCA). Therefore, the original solution had to be mimicked to be successful.

After considering this question some more, I think a key feature for this hypothesis to work is that the original function must be so integrated and vital for the biology of the organism that it must be mimicked/echoed to some extent. In terms of your RNA-example, it was not enought to evolve the ability to synthesize any complex molecule that could function as an enzyme and information carrier, but had to be RNA since this was already used in the biological pathways of the primitive organism.
With this in mind I think that you should look closely at vitamins (or other essential nutrients) for evidence of similar processes. The key think about vitamins is that they are often large complex molecules that are vital nutrients and the ability to synthesize vitamins differs widely between taxa. In a sense, the nucleotides were essential nutrients for the organisms in the proposed RNA-world, so vitamins/essential nutrients should be a relevant analog to look for similar evolutionary processes. However, keep in mind that molecular biology is not at all my field, and I might be mistaken on some aspects.
Take the example of Vitamin C. This cannot be synthezised by humans, but by most other mammals (vitamin C synthesis is considered ancestral in mammals). It can also be synthesized by plants, yeast and many other animals. However, vitamin C is used in different ways in different organisms. Plants use it e.g. for photosynthesis, photoprotection, cell wall growth and in the synthesis of plant hormones, while humans and other mammals use it as enzyme cofactors and for immune responses. Another key aspect is that plants, yeast and animals all use different pathways to synthezise vitamin C (Drouin et al, 2011), which indicates that the synthesis of vitamin C is not ancestral to all these taxa (i.e. not an ancestral feature of all eukaryotic life). In mammals, the synthesis of vitamin C has also switched between organs multiple times, which also indicates novel adaptations that results in the same molecule.
To me, it seems very likely that vitamin C was initially obtained by animals from plants (which have very high concentrations of vitamin C) as part of their diet (i.e. environmentally provided) and became an essential component in many biological pathways. If this is the case, animals later gained the ability to synthesize vitamin C themselves, using a different biological pathway than plants. This feature has later been secondarily lost (e.g. humans and teleost fish) and regained multiple times in different taxa. However, this is speculation on my part, and I don't know this literature well enought to say if there are studies on the origin of vitamin C synthesis in animals, or if the pathways of vitamin C synthesis in plants and animals are fundamentally related. A review by Smirnoff et al (2001) indicates that there are some similarities between the enzymes involved in the final stages of vitamin C synthesis:

The gene and/or cDNAs encoding GalLDH, GulLO, and AraLO have been isolated and described from several organisms including cauliflower, sweet potato (GalLDH, 54, 121), rat (GulLO, 70), and Saccharomyces cerevisiae (53). In addition, complete nucleotide coding sequences of the A. thaliana and Nicotiana tabacum GalLDH genes (Accession No. AB042279.1, AB024527.1), and the Candida albicans AraLO gene (Accession No. AF031228) have been submitted directly to GenBank and associated databases. The predicted amino acid sequences of these related proteins share substantial amounts of identity. The mature cauliflower GalLDH amino acid sequence shares 28% overall identity with the rat GulLO and 26% identity with the Candida albicans AraLO (using the J Hein method with PAM250 residue weight table).

However, this doesn't necessarily mean that the synthesis of vitamin C is ancestral to both plants and animals. I haven't been able to find any papers on the origin of vitamin C synthesis, and if there is evidence that it is ancestral to all modern life.
In either case, I think it could be useful for you to look closely at vitamins in animals or other organisms for possible examples of the type of processes you are looking for, since they are (by definition) essential nutrients that some animals can and others cannot synthesize. They should therefore be good potential targets to find similar processes as your RNA-example. Vitamin B12 is an extreme to the other end, since it is essential for most animals but can only be synthesized by bacteria (so the main source is through bacterial symbiosis).
It is also possible that I'm mistaken, and that synthesis of all vitamins is ancestral to modern life, and that there has only been subsequent loss of the ability to synthesize certain vitamins/nutrients. Helliwell et al (2013) mentions this as a possibility in relation to the RNA-world, but also points out that the pathways for biosynthesis often differs between taxa, which would suggest that there has indeed been secondary acquisition:

The fundamental nature of vitamins is illustrated by the close structural relation of many vitamins to nucleotides (Figure 1), reflecting the likelihood that they were present in the ancient RNA world. Yet, their biosynthetic pathways appear to have arisen via the patchwork model of pathway evolution [31], resulting in the recruitment of unrelated proteins in any one pathway. Indeed, many vitamins are synthesized by different routes in different organisms [20]. For example, alternative pathways are found for thiamine biosynthesis in prokaryotes and among different eukaryotes (Figure 2) [20]. Despite this diversity in biosynthetic pathways, there appear to be common trends in the causes and mechanisms underlying pathway loss.

I apologize if it is unsuitable to post this as a separate answer, instead of adding it to my previous answer/comment as an edit. However, I felt that they expressed very different ideas, and it felt more logical to keep them separate.