Thursday, 23 June 2011

$100 worth of science fail

So the Canadian government has decided to give our bills a makeover. Gone are the days of money made out of cotton! A new era of synthetic polymer bank notes has arrived. They look pretty cool, which is good. Supposedly, these notes are harder to counterfeit, which is even better. And the $100 bill is a celebration of science, which is even more awesome. The reverse side of the bill shows a bottle of insulin, a lady working at a microscope, and a strand of DNA, as shown below.

 Wait a second. Something looks wrong here. Let's take a closer look...


 That helix is left-handed! DNA is a right-handed helix, not a left-handed helix. I applaud the Government for making the bill science-centric, but really, how hard would it have been to get the art accurate? The left-handed helix mistake is incredibly common, but that's really no excuse.

Thursday, 16 June 2011

Wait...what?

Where do I even begin with this one?



You know what? I'm just going to let this picture do the talking.

Thursday, 9 June 2011

OM NOM NOM

From the journal Entomological Science (published online May 18th) comes this interesting predator-prey role reversal1:




Yes, that is a giant water beetle eating a turtle.

The photo was snapped by Shin-ya Ohba outside of Hyogo, Japan, while collecting samples for his research. While giant water beetles are known to chow down on smaller insects and small fish, finding one dining on a baby turtle is quite bizarre. Ohba writes:
"The bug inserted his proboscis into the neck of the turtle....Although I could not confirm whether the bug caught the turtle by himself in this observation, the dead body of the turtle was fresh. Probably, he had just captured the turtle. This is a first report of a Lethocerinae eating a turtle."
Pretty neat. And also pretty scary.

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1. S. Ohba . "Field observation of predation on a turtle by a giant water bug" . 2011 . Entomological Science . doi:10.1111/j.1479-8298.2011.00450.x

Sunday, 5 June 2011

This Week in Science (June 5, 2011)

Just a pair of papers for this week's TWIS. I haven't had much time to dedicate to reading new research this week, but I'll have more next week!

To start off, I'll point you in the direction of the infamous "arsenic bacteria" paper, which has finally been published in Science after languishing on Science's pre-print server for months. This paper, if you're unfamiliar with it, claimed to show the discovery of a new species of bacteria that utilized arsenic in its DNA rather than phosphorus. It was torn to shreds by critics due to problems in the authors' methodology and doubts about the results - and for good reason. Science's response to all the negative criticism that the paper has recieved has been to publish a list of criticisms (and the authors' responses) along with the paper. Jerry Coyne has a good rundown of the paper's publication on his blog.

Continuing on:

  • DNA computing and square roots  - Published this week in Science is a paper by L. Qian and E. Winfree detailing an interesting advancement in DNA computing. The authors were able to design and string together DNA logic gates to create a simple molecular computer able to calculate square roots. Creating a DNA logic gate is actually quite simple, and there are multiple ways it can be done. The authors did it by using a "seesaw gate"design: the gate consists of a short stretch of DNA that can pair with multiple different sequences. One such sequence is added as an "input", which competes and replaces a second sequence that is already bound to the gate. This replaced sequence becomes the "output", which is then free to act as an input for a second gate. Gates can be strung together to create more complicated systems. The authors devised a way to string such gates together to create a system that could calculate square roots. As cool as this is, though, this early biological calculator takes a while to complete calculations - up to eight hours. Nevertheless, this is a big step towards creating bigger and more powerful DNA computers. A more detailed summary of the paper has been posted on Wired, which I highly recommend, as they do a better job explaining logic gates than me!
(L. Qian and E. Winfree . "Scaling up digital circuit computation with DNA strand displacement cascades" . Science . 2011 . 332(6034): 1196-1201, doi: 10.1126/science.1200520)

  • Proteins successfully extracted from mammoth bones - A paper published this week1 in the journal Geochimica et Cosmochimica Acta describes the successful extraction of collagen protein from 600,000 year old mammoth bones. The authors were investigating the idea that peptide mass spec. could be used to identify fossils; that is, if you could determine the sequence of proteins in the fossil, you could compare the sequences to a database of known proteins. Finding proteins which are a close match would narrow down the identity of the fossils in question. To test this idea, the authors used bones from two mammoth fossils and one mastodon fossil. After grinding samples of the fossils into powder, they performed a series of chemical extractions and washes, then prepared them for mass spec. This allowed them to sequence the extracted protein, which was confirmed as collagen. The sequence data was good enough that the collagen - and consequently, the fossils - were correctly identified as being related to elephants. The authors were even able to use this data to distinguish the samples as elephantid (mammoth) or mammutid (mastodon). These findings are important for two reasons: first, they show that proteins can successfully be recovered from fossils as old as 600,000 years; and secondly, they demonstrate that protein mass spec. can be used to correctly identify ancient fossils (or at the very least, identify the closest living relative). Exciting indeed!
(M. Buckley, N. Larkin, and M. Collins . "Mammoth and Mastodon collagen sequences; survival and utility" . Geochemica et Cosmochimica Acta . 2011 . 75(7): 2007-2016

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1. This paper actually wasn't published this week, it was published in April. For whatever reason, it looks like it only made the news now.

Sunday, 29 May 2011

Fir-Tex: Bullshit in vest form.

Move over Q-ray, there's a new nonsense product in town.

Everyone is familiar with Q-Ray bracelets. Little more than two ball bearings attached with a piece of steel cable, Q-Ray bracelets are marketed as some sort of mystical device that will revitalize your "bio-energy" (whatever that means). Despite being a known fraud, the Q-Ray bracelet remains popular. In the face of mounting evidence that it's a load of baloney, we've seen the nonsense "bio-energy" fad expand in the last year. Products like the phony Power Balance bracelets have hit the market (and like the Q-Ray before it, have been debunked a thousand times over by the skeptic community). But if you've ever said to yourself "I really wish I had a similar product that covered my entire torso", then you've been out of luck.

Until now.

Introducing "Fir-Tex", the latest in wallet-draining pseudoscientific technology. Fir-Tex claims to be the first "energized textile", that can be fashioned into clothing. Products such as Wear Wings - brought to you by Red Bull - are being marketed as the world's first in "energy fashion". Having a slow day? Feeling drained at work? Don't worry, just send in a big cheque, pull a Fir-Tex vest on over your body and your motor will be revving like a chihuahua on speed.

But how does it work? Or better yet, does it work?

Bold Claims
Before we get into the "science" behind Fir-Tex, let's take a look at just what the product has been claimed to do. A banner at the bottom of the Fir-Tex splash page tells us that Fir-Tex clothing will "improve energy and wellbeing", allow you to "jump 10% higher", "improve performance", "boost power by 10%" and "optimize balance and microcirculation". These claims are pretty generic as far as "energized" products go. You'll see similar claims made for Power Balance and Q-Ray bracelets. Also note that claims like these are incredibly ambiguous. What exactly does "improved wellbeing" mean? How do you "optimize" microcirculation? How do you "boost" power, and for that matter, how do you measure power in order to determine that it's been boosted? These claims are little more than technobabble; they're utterly meaningless strings of sciency-sounding words. Just how ridiculous the Fir-Tex gobbledygook is can easily be illustrated. Of the following three items, one is related to Fir-Tex and the other two are taken from Star Trek. Can you tell which is which?
  • decyon field fluctuations
  • biogenic energy in the 40 to 50 micron range
  • aggregate field of plain polarization
Fir-Tex stops short of making  any sort of medical claims, however. They're probably aware of how Q-Ray's medical claims worked out (very poorly), and to avoid lawsuits, they've added a disclaimer to their site:
"So by entering this website you must first acknowledge that FIR-TEX has not been designed for and does not make any claims whatsoever to be any kind of medical cure. Because it isn’t! The aim of FIR-TEX is to bring technological fabrics on the market and their products will help some subjects to simply perform better or feel better while others won't experience any difference or could even feel discomfort."
So despite their claims of "increased performance", they acknowledge that "others won't experience any difference". How convenient. If Fir-Tex doesn't work for you, it doesn't mean the product is a fraud, it just means that you're different.

But enough about bogus product claims, let's get down to some science.

Im in ur body vibratin ur waterz
So how does Fir-Tex work? Luckily for us, the Fir-Tex site has a science section. According to their site, Fir-Tex works on the principle of Far Infrared Rays. These are energetic rays that lay just outside the visible spectrum. They have wavelengths greater than that of visible light, but shorter than that of microwaves. What do far infrared rays do? Well, I'll let the Fir-Tex folks explain it to you:
"The human body is a reservoir of all kinds of bio-toxins which cannot be expelled immediately and become stored in the body, thereby triggering illness. When toxic gases such as sulfur dioxide and carbon dioxide, or potentially fatal heavy metal toxins such as mercury, lead and chlorine, meet large water molecules, they are encapsulated by clusters of water and trapped in the body. Where these toxins are accumulated, blood circulation is blocked and cellular energy is impaired. However, when a 7 to 11 micron FIR wave is applied to these large water molecules, the water begins to vibrate. This vibration reduces the ion bonds of the atoms which are holding together the molecules of water. As the water evaporates, the encapsulated gas and toxins can be released and this is exactly what FIR technologies can do for the human body."

Wait....what? It took me a few times to read that paragraph to understand what they're trying to say. From what I understand, it's this: "bio-toxins" accumulate in your body by being "encapsulated" by water, and causing illness. FIR "vibrates" the water, "reducing" the ion bonds, causing the water in your body to evaporate and setting the toxins free so they can be expelled from the body.



This paragraph also represents a massive chemistry fail. When toxins enter your body, they do not become "encapsulated" by water molecules. This is another instance of technobabble - water cannot "encapsulate" anything, let alone toxins1. Perhaps they mean that toxins will bind with water molecules, but this won't happen either. Water molecules won't bind with gasses, nor will water bind with mercury.

The paragraph continues to tell us that applying far infrared rays to water, the molecules will vibrate, and this vibration "reduces the ion bonds". They're correct in stating that applying far infrared rays will cause the water molecules to vibrate; this is because applying ANY kind of energy will make water molecules vibrate. Think back to junior high chemistry class. When you apply energy to molecules, what happens? They speed up, move around faster, begin to vibrate more. If you put a glass of water in the microwave, what will happen? It boils. The microwave radiation increases the energy of the water molecules and they start moving faster and faster. Applying infrared radiation is no different - it increases the energy of the water molecules and they will move around faster. This is the whole idea behind the infrared heat lamps you see keeping the burgers warm at McDonald's. So while infrared rays will make water vibrate, they aren't special in their ability to do this.

Furthermore, even though infrared heat can get water vibrating faster, it won't "reduce the ion bonds of the atoms which are holding together the molecules of water" because water does not contain ionic bonds. All bonds are not the same. Some bonds have more energy than others. Some bonds are made by sharing electrons between atoms, while some are made by the transfer of an electron from one atom to another. The different types of chemical bonds are given different names to distinguish them from one another. Ionic bonds are once such type of bond. They're formed by the electrostatic attraction of two differently charged ions. Sodium ions and chloride ions will forms ionic bonds and produce salt, for example. Water does NOT form ionic bonds. Water forms hydrogen bonds. These are a very different type of bond.

But perhaps that's just semantics. The point Fir-Tex makes is that applying far infrared rays will make the water molecules in your body evapourate, and allow toxins to be removed. Now, if you don't immediately see how that incredibly terrible that is, then read it again. Let's ignore the fact that it would take an extraordinary amount of radiation to make the water molecules evapourate. Considering how important water is for the proper functioning of your body, does evapourating the water from your very tissues sound like a good idea? And, if the water is supposedly "encapsulating" toxins, wouldn't freeing them from the ensnaring water molecules be even worse? Then they would have free reign to move about your body. Take mercury as an example, since it is one of the toxins mentioned by Fir-Tex above. Mercury does its damage by accumulating in neurons and inhibiting the formation of myelin. At high concentrations, it can cause severe impairment of mental faculties and can potentially be fatal. If mercury were "encapsulated" by water molecules in the blood, it would actually prevent mercury from reaching your central nervous system and doing damage. Fir-Tex products would actually be doing more harm than good!

It's also interesting to note that Fir-Tex is not the only "far-infrared technology" on the market. However, Fir-Tex does claim to be "different" from all those other products. How is it different? Well, Fir-Tex doesn't seem to want us to know:
"During our meetings with our customers we explain the difference between our product/technology and any other product using FIR technologies. The technical information is not public for the moment for obvious reasons which one would of course understand."
No, actually, I don't understand.

So the principle by which far-infrared technology is supposed to rely on is nonsensical at best and utterly batshit-stupid at worst. Does Fir-Tex have any evidence that it works?


Science, schmience. We use Chinese medicine!
The Fir-Tex website's science section has a page called "Live Blood Analysis", which they present as scientific evidence that their product works. I'll get to that in the following section. What I want to go through first is this "scientific presentation" that can be found on their website.

The presentation begins with a summary of infrared rays. They claim that infrared rays are "most beneficial" for "the living beings". In what ways they are "most beneficial" is not explained. They do, however, give three properties of infrared rays. First, they "can generate heat by direct irradiation but localized objects can also reflect them". Well, so can microwaves, but sitting next to a microwave tower is a bad idea. In fact, that's WHY it's a bad idea. Secondly, they "deeply penetrate the living tissues". Well, so can X-rays, but again, basking in X-rays isn't a good idea either. And finally - and this one's a doozy - they "activate (water) molecules, increasing overall temperature of the system". Increasing the overall temperature of the system is the same thing as generating heat, mentioned in the first point. But what does it mean to "activate" water molecules. Are all the water molecules in your body normally "inactive"? How do they become "active" in the presence of infrared rays? This is yet more technobabble (sensing a theme here?). These three properties, Fir-Tex says, are why far infrared rays are called “bio-genetic rays” (another made-up word).

Continuing on, Fir-Tex evokes Wein's displacement law as some sort of justification for their claims. Wein's Law takes the form of λ=K/T, where T is temperature in degrees Kelvin, λ is wavelength in nm, and K is a constant, equal to about 2.896x10-3m.K. Using this equation, Fir-Tex calculated the "frequency of emitted radiation" at 35°C as 9.4μm. If you whip out your calculator, you'll see that their math checks out. Human bodies (at 37°C, not 35°C, but whatever) do emit infrared heat at about 10μm, and this is what IR cameras are calibrated to measure. Armed with this number, what does Fir-Tex do? They conclude that "this explains why human body [sic] easily absorbs far infrared rays between 4 and 16 microns". Holy non sequitor, Batman! Using Wein's law shows what wavelength the human body emits, but says nothing about what wavelength it absorbs. And even if it did show that the body absorbs light of a certain wavelength, how does that show it is the "most easily" absorbed wavelength? What would that even mean?

What does any of this have to do with Fir-Tex's brand of far infrared technology? Well, as the presentation points out, our bodies are composed of large amounts of water. Infrared radiation can make water warmer. Fir-Tex
"works like an active mirror; it captures/receives the thermal radiations from the body heat. Then it reacts and uses these thermal/Far Infrared rays (rays of life) to send energy back into the body with multiple beneficial consequences on cells and tissues."
In other words, Fir-Tex is the world's most expensive blanket! All it purports to do is trap the heat radiated by your body. The same effect can be achieved by a wool blanket. $30 at Bed Bath and Beyond and you can be soaking in all the Rays of Life (whatever that means) that you want.

But Fir-Tex is firm in their belief that infrared radiation is beneficial. Afterall, it's what Qigong masters use!
"Energy medicine is very old, at least as old as the first Qigong masters and other ancient practitioners of healing touch therapies. These healers all had in common the ability to emit energy through their hands, and so do many modern day healers, such as Dolores Krieger, Ph.D., R.N., who began teaching healing touch techniques in the U.S. in the 1970s. Contemporary researchers have now proved that these forms of energy medicine use wavelengths in the infrared range."
Qigong "healers'" hands emit radiation in the infrared range? Does this come as a surprise to them? That's the range at which everyone's body emits radiation. That's what the Wein's equation above showed!

But none of this actually shows that Fir-Tex works at all. Fir-Tex's supposed evidence can be found in the Live Blood Analysis section of their Science page.

Live Blood Analysis, or How Not to do a Scientific Study
Prior to this, I had not heard of Live Blood Analysis (LBA). I'm more than familiar with haemotological techniques, but Life Blood Analysis was not a technique that I knew. A few minutes on Google, and I discovered that LBA is a technique pioneered by a company called Sevenpointfive. Who's Sevenpointfive, you ask? They're a South African naturophathic company that pushes their brand of "natural supplements". They present the same, tired "modern medicine is wrong, buy our products instead" line as every other "natural supplement" company. Their schtick, though, seems to be their LBA technique. What they do is simple. They take a drop of your blood, and look at it under a microscope for "imbalances" and "deficiencies". Whether or not Sevenpointfive's "technicians" can accurately diagnose physiological conditions using LBA is rather dubious to me. As far as I can tell, LBA is not a proper technique used by the medical community.

It's this exact method that Fir-Tex used to test their product. They took blood samples of individuals, then gave them all Fir-Tex vests to wear for 10 minutes, and took another sample. Then they compared the two. That is as detailed as their test gets. There's a huge problem here: they didn't use a  negative control subject (or if they did, they never mentioned it or showed the results)! This is a gigantic experimental flaw, and any results from their tests are worthless because of it. They also make no mention of what kind of activities the subjects were doing when they were using the Fir-Tex vests? Were they sitting still for ten minutes? Were they exercising? Was this controlled at all? Their methodology is severely lacking. Such a study would never get published in any reputable medical journal, which is probably why it exists only on the Fir-Tex website.

What were the results of their "tests"? Well, I haven't the slightest clue. Take a look at what they present as evidence:

Maybe it's because I don't have sufficient training to understand what I'm looking at, but I don't see a significant difference in the two treatments. All I see are alot of erythrocytes with some platelets here and there, in both cases. Nevertheless, Fir-Tex claims results like these indicate that their product protects cells from damage from free radicals (free radicals, according to Fir-Tex, are "atoms that are missing ions", a laughably stupid statement), reduces cholesterol, and boosts the immune system. None of their LBA pictures indicate any of these things. It is interesting to note that Fit-Tex admits "that each individual reacts differently to the same treatment, the results are thus never the same", but they don't accept this as evidence that their product does nothing. Quite to the contrary, they take this as evidence that Fir-Tex does work, just in different ways in different people. These tests definitely do not bolster their earlier claims of increasing your jump height by 10%, or "optimizing your balance". And even if they DID show such results, we have no way of knowing any of this is attributable to the Fir-Tex vests because of their shoddy methodology!

No doctor worth their medical degree would produce a medical study as awful as this. So who is responsible? Fir-Tex informs us that the tests were performed by "Dr Annelise Bunce, certified Clinical Metal Toxicologist and certified Dark Field and Multi Phase Microscopy and expert in Live Blood Analysis". Here is her CV. Masters in homeopathy? Oooh. That explains it.

More money than sense
So just what will one of these babies set you back? Between €325 and €475 (that's $453CAN to $663CAN). Hell, while you're at it, €525 will get you a saddle for your horse. This is an unbelievably colossal waste of money. Fir-Tex does nothing more than make you warm. The "science" behind it is complete and utter nonsense, none of their claims can be validated and it simply does not work. Just like the Power Balance and the Q-Ray before it, Fir-Tex is a scam that will have its manufacturers laughing all the way to the bank.


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1. It's been brought to my attention that this point is not entirely correct. Water molecules can, in fact, "encapsulate" some ions. This is called a "solvation shell". It occurs when a positively charged ion is attracted to the electrostatically negative oxygen of water molecules. Water molecules will effectively form a shell around the ion. I have my doubts about whether water can form a solvation shell around toxins, which are rather large compounds. Perhaps a more chemistry-minded reader could clarify this.

Thursday, 26 May 2011

Central Dogma not so challenged after all?

In last week's This Week In Science, I summed up a paper published in Scicence by Li et al.1 which was hyped up as being a challenge to the Central Dogma of molecular biology. The authors compared the RNA sequences from numerous individuals to the original DNA sequences they were derived from. What they found were a multitude of sites where the RNA sequences differed from that which would be expected given the original DNA sequence. Moreover, these variations were shared across individuals, indicating that they were not likely due to random mutation. Furthermore, the team found proteins that matched the varied RNA sequences and not the DNA sequences. These results suggested that there exists some yet unknown editing step during transcription that alters individual nucleotides in the resulting RNA transcripts.

However, declaring the Central Dogma to be toppled may have been a bit premature. According to Lior Pachter at the University of California, Berkley, the variations discovered by the researchers could be artifacts caused by their sequencing equipment. Many of the sites that were found to contain altered nucleotides lie in regions which are known to often cause RNA sequencing errors. In other words, the variations that the team observed, in many cases, might just be sequencing mistakes. 

Further skepticism has been shown by Joe Pickrell at the blog Genomes Unzipped (which I highly suggest reading, as he goes into quite a bit more detail than what I've presented below). He points out that the differences in RNA and DNA that the authors discovered might be false positives created by attributing a particular RNA sequence to the incorrect DNA sequence. For any given DNA sequence, there are bound to be other sequences very similar - even almost identical - to it2. If you are given an RNA sequence, then, how do you determine which of the very similar DNA sequences it is derived from? Unless one takes steps to remove the incorrect sequences, it is very likely that you will end up with a false-positive. It would appear that Li et al. did not take such steps.

Pickrell points out another problem with sequencing and mapping through RNA splice sites. Mammalian genes are frequently alternatively spliced, and a cDNA library like the ones Li et al. used will have multiple isoforms of a gene. When mapping such transcripts back to the genome, you have to keep in mind that the genomic sequence will still contain the introns that have been excised in the mature mRNA transcripts. If you compare the shorter, edited mRNA to the longer, unedited DNA, you're likely to find many differences between the two. Mapping a particular sequence read to the wrong isoform will generate false-positives. Pickrell shows that Li et al. did just this on at least one occasion.

So widespread RNA editing in humans might not be a reality. It's possible that it is, but problems with the procedure used by Li et al. raise many doubts. I'm looking forward to reading the follow-up research. Until then, as perhaps Mark Twain would say, reports of the death of the Central Dogma have been exaggerated.

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1. M. Li et al. "Widespread RNA and DNA sequence differences in the human transcriptome". 2011. Science. doi:10.1126/science.1207018

2. It should be obvious that the larger the given sequence, the fewer (near)identical sites there will be.

Tuesday, 24 May 2011

This Week in Science! (May 22, 2011)

This week1 saw quite a few interesting papers in biology. Here's a few that caught my attention:

  • Mammalian brain evolution driven by smell - One of the biggest characteristics that distinguish mammals from other animals is that we have relatively large brains in relation to body size. Just why mammals evolved rather large brains has been a point of speculation, but a paper published in Science this week suggests that a reliance on our sense of smell resulted in our bulging brains. The research by T. Rowe et al. involved examining the fossils of two species of Jurassic cryodonts, the group of ancient reptiles which would diverge to become the mammalian lineage. They used a technique called X-ray computed tomography to reconstruct endocasts of the cryodont brains, and compared them to those of earlier, Triassic cryodonts. They first looked at the endocast from Morganucondon oehleri, and noted that the brain was 50% larger than in earlier cryodonts. But there were other important differences: the olfactory bulbs were larger, there was expansion in the cerebral hemisphere, and the cerebellum extended to cover the midbrain. They next looked at the endocast from Hadrocodium wui, the closest known fossil to living mammals. They observed another 50% increase in brain size, with even larger cerebral hemisphere and olfactory bulbs. These observations lead the team to speculate that increased dependence on olfaction drove the evolution of larger brain sizes in early mammals. Given that early mammals were likely nocturnal, and had to rummage around in the dark for food, this idea does make sense. The researchers are now looking for evidence that might indicate that early mammals were indeed nocturnal.   
(T. Rowe et al. "Fossil evidence on origin of the Mammalian brain" 2011. Science. 332(6032): 955-957)
  • Another strike against the Central Dogma - Every student in biology is brought up to know the "Central Dogma" - the idea that can be summed up as "DNA encodes RNA encodes protein". This is not a had and fast rule, though, and the discovery of things like ribozymes have shown the Central Dogma to be less dogmatic. A new paper published in Science this week furthers this point. A team of researchers lead by M. Li from the University of Pennsylvania in Philadelphia compared the DNA sequences from 27 different individuals to their corresponding RNA sequences. In a very large number of cases, they discovered that the RNA sequences that had been transcribed from the DNA sequences were different than would be expected; that is, the RNA sequences contained sites where the nucleotides had been changed. These changes in RNA sequences were shared across many of the individuals studied, indicating that the changes were not likely due to random mutation. Furthermore, using mass spectroscopy, they found peptides whose sequences reflected the RNA variant sequences rather than the original DNA sequences. What all of this suggests is that the DNA-RNA-Protein relationship is not as strict as previously thought. The DNA sequence of a gene might not dictate the exact composition of it's gene product after all. 
(M. Li et al. "Widespread RNA and DNA sequence differences in the human transcriptome". 2011. Science. doi:10.1126/science.1207018)
  •  Extinction rates may be overestimated - Estimating extinction rates is an important part of ecological conservation, but unfortunately, there is really no reliable way of directly determining such rates. Instead, researchers often rely on indirect methods, but this can run into problems. One popular indirect method is to observe the number of different species found as your area of study gets larger (called a species-area accumulation curve), and then extrapolating backwards to successively smaller and smaller areas to determine the rate at which species number decreases. A new paper in Nature by Fangliang He and Stephen Hubbell argue that this method routinely overestimates extinction rates (sometimes by as much as 160%!). This comes as both good news and bad news; it means that species loss due to habitat destruction in some areas might not be as high as previously estimated, but it also means a more accurate method for estimating extinction rates needs to be devised in order to develop optimal conservation projects. 
(F. He and S. Hubbell. "Species-area relationships always overestimate extinction rates from habitat loss". 2011. Nature 473: 368-371. doi:10.1038/nature09985)

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1. Yeah, I am aware I'm posting this a little late. So sue me.

    Saturday, 14 May 2011

    From Embryo to Adult: Body Plan Patterning in Drosophila - Part I

    Take a look at a fly and it won't be long until you realize that even such a relatively simple creature is quite complex. This issue of complexity is a talking point for creationist rhetoric; "How can such complex structures just come together to create a fully formed individual?" they muse, "It must be the work of a divine creator!" Unfortunately for them, the process of development is well known and thoroughly understood. In a series of posts, I'll attempt to dispel this myth, and show just how a complex life form can arise from a single simple cell by entirely natural means. In this first part, I will introduce the concept of maternal effect genes, and one of the most important such gene, bicoid.

    The development from a single egg to a full adult fly is a long one, but the process begins long before fertilization ever occurs. Consider, for a moment, the process of fertilization in humans. In humans, the egg cell is monstrous in size compared to the relatively diminutive sperm cell. There is much more cytoplasm in an egg than in sperm, and that cytoplasm is full of mRNA, mitochondria and other cytoplasmic factors. These are ultimately donated to the embryo upon fertilization: the fertilized embryo contains nuclear genetic information from both parents, but contains cytoplasmic factors from the mother alone.

    Drosophila are no different. The unfertilized egg is not just a storage container for nuclear DNA, but it contains mitochondria and mRNA which will ultimately become part of the embryo after fertilization. Many of those mRNA transcripts belong to a class of genes that is very important to the development of the body plan: maternal effect genes.

    Maternal effect genes get their name from the fact that they are expressed in the mother, and not in the embryo. During oogenesis, the tissues in the ovary express these genes, and the transcripts are packaged into the embryo. This is in contrast to zygotic genes, which are expressed in the nuclei of the embryo itself. One thing that makes maternal effect genes so interesting is that individual females that are mutant in such genes are phenotypically normal: the phenotype shows up in the progeny instead1. There are about 50 maternal effect genes that play a role in the development of the Drosophila body plan, and they set up the basic framework for the zygotic genes that come later (which I will describe in a later part). Perhaps the biggest role they play, though, is in setting up the body plan axes.

    The Drosophila embryo has two axes: the anterior-posterior axis, and the dorsal-ventral axis (see Figure 1). If the the adult body plan is to be laid out in the developing embryo, it is important to make sure the embryo knows which side is which (you don't want the head to end up on the wrong end, for instance), and this is the primary goal for many maternal effect genes. The first of such genes that comes into play is called bicoid, and it works to determine the anterior-posterior axis of the egg. It does this through morphogenic gradients, a concept that you'll see used extensively throughout development.

    Early on in the investigation of body plan development, it was noted that those mothers who are bicoid mutants give rise to progeny without properly differentiated anterior ends (they lack a head or thorax). This fact was interesting itself, but a series of experiments made the fact all the more striking. If you take an unfertilized Drosophila egg and poke the anterior end with a needle, allowing some of the cytoplasm to leak out, they end up developing into embryos that resemble those from bicoid mutants. Furthermore, if you were to transfer cytoplasm from the anterior end of a wild-type egg to the anterior end of a bicoid mutant egg, the embryos would develop normally2. It was also found that if the cytoplasm from the anterior end of a wild-type egg were transferred to the middle of a bicoid mutant egg, the embryos would develop a head right in the middle. This immediately suggested that there was some cytoplasmic factor in the anterior end of the egg that was lacking in bicoid mutant eggs, and this factor was responsible for establishing which end of the embryo became the anterior end.

    If you were to look at the distribution of bicoid mRNA in the unfertilized egg, you would see just that (Figure 2). Before fertilization, bicoid mRNA is concentrated in anterior end. It remains untranslated until fertilization occurs. Upon fertilization, translation begins, and Bicoid protein diffuses through the embryo. Bicoid, then, forms a gradient, with high concentrations at the anterior end and low concentrations at the posterior end. Regions with a high concentration of Bicoid protein develop anterior structures, and the regions with a low concentration of Bicoid protein develop into posterior structures. The precise function of Bicoid will be explained in a later post, but for the moment, it is sufficient to know that bicoid activates particular zygotic genes in a concentration-dependant manner. Different zygotic genes have different threshold levels for activation, so the concentration of Bicoid across the embryo will determine which zygotic genes get activated, and in turn, determines what each region of the embryo develops into. This is the key principal behind a morphogenic gradient.

    But bicoid isn't the only maternal effect gene that plays a role in setting up the anterior-posterior axis. In the next part to this series, I will discuss three more important maternal effect genes: nanos, caudal, and hunchback.

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    1. If this seems confusing, remember that the genes are expressed in the mother, but the transcripts, and ultimately, the gene products, are packaged in the egg. If a maternal effect gene is mutated, the mother will be fine, but her progeny will not, because it is the eggs that are receiving the defective gene products.

    2. This type of experiment is called a "rescue experiment", because it allows one to "rescue" the mutant embryos and allow them to develop normally.

    From Embryo to Adult: Body Plan Patterning in Drosophila

    How a fully formed organism develops from a single fertilized egg cell is a complex process. That process is no less complex in inverterbrates than in verterbrates, and much is known about just how development occurs in Drosophila. In the following series of posts, I'll detail the just how you can get a complete fly from a simple cell.

    (Links will be available as I write and post each individual part)

    Part II: Setting up the Anterior - Posterior Axis: Hunchback, Nanos & Caudal
    Part III: The Terminators
    Part IV: Setting up the Dorsal-Ventral Axis: Spätzle, Toll and Dorsal
    Part V: Zygotic Gene Expression along the D-V Axis
    Part VI: Gap-gene Expression
    Part VII: TBD