How many Genes? A Short History of Off-Target Estimates

The late Lewis Thomas referred to medicine as the youngest science. In essence, medicine is a combination of sciences and techniques,  an ensemble which mutates faster than the key concepts of more mature fields like physics and chemistry. In biology, while most of our knowledge about the types of cell organelles or the number of human bones won’t change radically in the future, the same cannot be said about the branch of genetics.

NyTimesI was reminded of that while looking at the front page article of the New York Times from 1978, “Doctors Isolate a Gene, Allowing Birth Defect-Detection”. The article mentions a scientists’ estimate of 3 to 4 million genes per cell.  About 13 years earlier, the “genetic code” had been cracked. But in discovering the triplet codes used by DNA and messenger RNA in transcribing and translating, respectively, biologists had only figured out how the cell knew which amino acids to use and how to bond them in the correct order while assembling proteins.They had no idea of how long each set of instructions(gene) was or how many genes  were programming for those large versatile macromolecules known as proteins, essentially about 50% of the cell’s dry weight.

The first wild guesses of  the 1960s about the number of genes in humans was based on the number of nucleotide bases and it was in the order of 6 to 7 million. Once they started to isolate genes (at the time of that NY Times article) and by the time they initiated the human genome project in 1990, which eventually did a base sequence of all of our DNA, the estimate had come down to 100 000. Over a decade later, a refined analysis led to a revised total of no more than one fifth of that. In fact, the lowest estimate has now come down to about 17000.

To see another reason why the gene total was exaggerated, we have to look at introns. Interestingly in 1977, a year before the printing of this article, introns had been discovered independently by a pair of future Nobelists, Phillip Sharp and Richard Roberts. It turned out that these introns, 98% of the DNA base sequences, did not actually show up on the messenger RNA. Only a small fraction was actually coding for proteins. Some scientists even made the blunder of dubbing it “junk DNA”. But nothing could be further from our current approximation of the truth. Now called intergenic DNA, here’s what it does:

(1) It plays a key role in regulation of reactions in a cell, controlling which genes are turned “on” or “off” at any given time. In essence intergenic DNA takes on a role previously assumed to belong only to protein regulators.

(2) It’s also responsible for “alternative splicing,” This involves combining different coding areas of a gene that are in between the non-coding zones, allowing more than one protein to be made from a single gene. Since there isn’t a gene behind every version of a protein, it reduces the required number of coding ones.

Because of the way the topic of genes is still covered in most high schools, the public still has some serious misconceptions about genes. Most human traits are not controlled by Mendelian inheritance. There are only a handful of characteristics that can be explained by dominant and recessive alleles. Even for something as relatively superficial as height, it is a trait controlled by many genes. Equally important is that the expression of these genes is strongly influenced by diet. The inheritance of eye color is also complicated. Eye colors have been divided into nine categories and a pair of genes on chromosome 15 play a major role in determining their color. However, it’s also influenced by a variation in at least 10 other genes, plus complicated interactions between these genes.(reviewed in Sturm and Larsson 2009, with more recent results in Liu et al. 2010 and Pospiech et al. 2011). 

Returning to the NY Times article, the anemias referred to were thalassemias. According to an New England Journal of Medicine article published on that same day, the gene identified led to the detection of a thalassemia-type from amniotic fluid. Thalassemias are molecular diseases—either a pair of genes for two of hemoglobin’s four protein chains is missing (alpha form) or one to two genes is altered (beta form). These diseases occur most often among people of Italian, Greek, Middle Eastern, Southern Asian, and African descent, in areas endemic to malaria. The concentration of the disorders is connected to the fact that that thalassemia genes offer some protection against the malaria parasite. Currently, if parents are predisposed to the disease, they are given genetic counselling. For women who already pregnant tests done on amoniotic fluid or tissue reveal whether the baby has a form of thalassemia and the potential severity.

The gene therapy and correction of the disorder that was envisioned in the 1980s has yet to materialize. Nature’s genetic secrets run deeper than we imagined. And as Eric Lander formerly of the Human genome Project said, “Going from the germ theory of disease to antibiotics that saved people’s lives took 60 years. We might beat that. But anybody who thought in the year 2000 that we’d see cures in 2010 was smoking something.”

Or believing what he read in the media.

Sources:

Stanford Tech: Understanding Genetics 

BioMed Central

MIT Technology Review

New England Journal of Medicine

α+ -Thalassemia and Protection from Malaria

National Institute of Health 

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Cheap Oil Prices, Not Good for Bioethylene

ethyleneI’m worried about the impact that low oil prices will have on the production of bioethylene and bioplastics. Bioethylene is made from sugars. Currently, ethane, a component of natural gas, serves as a bigger source of the gas ethylene (C2H4), while most of the world production is based on the cracking of large petroleum molecules. Crude oil is distilled into things like jet fuel, gasoline, lubricants and a 5 to 12-carbon mixture known as naphta. Then the naphta is “cracked”, essentially broken into smaller molecules. One of the latter is  C2H4is used as the raw material for many plastics such as low density polyethylene and the more recyclable high density polyethylene. Because all petro-products, including C2H4, are created in such large quantities, mass production drives down the price of plastics. Unfortunately, the whole process also makes a large carbon and ecological footprint, not to mention that inexpensive plastic also encourages the overproduction of some trivial products that generate needless waste.

Compared to petrochemical production, sugarcane-based bioethylene production in Brazil produces 40% less greenhouse gas emissions.  Ethanol is first produced from fermenting sugars. After purification of the alcohol, catalysts chemically dehydrate ethanol to ethylene.

The conversion of ethanol to ethylene is a dehydration. the catalyst is not consumed in the reaction, so it is not shown in the equation.

Finally the same technology is used to polymerize ethylene or its derivatives into a wide array of plastics. In essence then, the prefix in “bioethylene” and “bioplastics” is just used to identify the origin of their raw material.

bioethylene

Since sugar is the source of the ethylene, it is dubbed a “bioethylene”, and the polyethylene made by conventional methods is called a “bioplastic”.

It currently costs about $1,200 US to make a metric ton of bio-ethylene, which only competes with the petro-process when crude sells at over $100 per barrel. Even when oil prices were high, the top biological producer in the world, the Brazilian company Braskem, was producing only 1/20th of the amount made by Saudi Arabia’s two largest petro-producers. Now that crude has tumbled to below $50, neither Taiwan nor Alberta, the world’s two largest ethylene producers, is exactly looking over their shoulder. Meanwhile, chemically, it is possible to develop even more efficient, longer-lasting dehydrating catalysts that will work at still lower temperatures.

Critics of bioethylene point out that reliance on such a means can compete for the availability of arable land for food and animal-feed production and for the conversion of forests into agricultural land. It’s a valid criticism when corn is used. But in Brazil, the percentage of sugar crops currently devoted to bioplastics is less than 1%. In addition, land use would not suffer if eating habits in the industrial world improved, and if we replaced some of the sugar production intended for soft drinks and snacks with what’s necessary to generate plastics for medical devices and other important consumer goods.

It’s no secret that oil production has been recently manipulated by OPEC so that decreasing prices put pressure on Russia and especially on fracking in the United States. That not only makes it difficult on the bioethylene economy, but it hampers sustainable energy development such as solar and wind and encourages people to buy even less ecological cars. It’s a another somber reminder of the towering obstacles faced by a revolution towards sustainable development .

Sources:

Ethylene Formation by Catalytic Dehydration of Ethanol with
Industrial Considerations

Production of Bioethylene: Technology Brief 

Cracking of Petroleum

Onions: Don’t Dig and the Truth Remains Buried

?????????????????????????????????????????????????A great deal has been written about why onions make you cry, but the information contradicts. And how we’ll arrive at the truth might prove to be more fun than knowing the fact itself.

The 2012 chemistry textbook, General, Organic and Biological Chemistry, by H. Stephen Stokes; a PBS site, and chemistry.about.com all claim that, after the volatile lachrymator propanethial-S-oxide is produced by a cut onion’s enzymes,  it reacts with water in the eyes to produce the irritant sulfuric acid. But Scientific American, Molecule of the Month and the analytical services of onionlabs.com attribute the lacrimatory  effects directly to the molecule’s action on receptors. Sulfuric acid is not part of the explanation. From the latter:

LF is the chemical compound which directly causes the eye to tear (often called the onion lachrymator) and the chemical sensation of heat or mouth burn when an onion is eaten. It is measured using HPGC equipment and is reported in µmoles of LF/ml of onion juice. . ..

And then the details from a researcher writing in Scientific American:

The cornea is densely populated with sensory fibers of the ciliary nerve, a branch of the massive trigeminal nerve that brings touch, temperature and pain sensations from the face and front of the head. The cornea also receives a smaller number of autonomic motor fibers that activate the lachrymal (tear) glands. Free nerve endings detect syn-propanethial-S-oxide on the cornea and drive activity in the ciliary nerve–which the central nervous system interprets as a burning sensation–in proportion to the compound’s concentration. This nerve activity reflexively activates the autonomic fibers, which then carry a signal back to the eye ordering the lachrymal glands to wash the irritant away.

I started to get dubious about the alleged formation of sulfuric acid for the following reason. If, in the presence of water in the eye, the lachrymator degrades so quickly, wouldn’t most of the propanethial-S-oxide break down in the onion’s aqueous environment? Let’s assume for a moment that some still escapes unscathed due to its relatively high vapor pressure(v.p.) of 41.2 ± 0.2 mm Hg at 25°C. To put that in perspective, water’s v.p. is only 23.8 mm Hg at that temperature, so it’s about as volatile as ethyl alcohol whose vapor pressure is about 44 mm Hg.

onionsTo  look for any pH-changes, I taped only the ends of a wet piece of litmus paper in a sealed plastic bag. I chopped an onion and quickly placed the pieces into a ziploc, making sure that the acidic juices of the onion would not be in contact with the litmus. If the lachrymator indeed broke down into compounds that included sulfuric acid, then the exposed wet litmus should turn red between 30 seconds and couple of minutes, the time that it takes for the compound to form and reach the eyes. But there was no color change, consistent with the fact that the lachrymator itself has no pKa, a measure of acidic strength.

One could argue that the amount of acid produced was too small to affect the litmus. This research paper mentions that each milliliter of onion juice contains 1−22 μmol of the lachrymator. Let’s assume a density of 1.0 g/ml and an average mass of 120 g per onion, which is about 90% water, and that about only 30% of the lachrymator reached half a ml of water on the litmus. If it had  produced H2SO4 in a 1:1 ratio*, then we could easily calculate that we’d end up with a pH between 3 and 4, enough to turn the litmus red. (*Only one source (the textbook) had included a chemical equation, and it was not even balanced.)

I also mixed a small amount of vinegar with the onions, and within a few minutes, the same wet litmus did indeed turn red, revealing that the simple setup could detect acidity.

Z-propanethial-S-oxide makes up 95% of the lachrymator

Z-propanethial-S-oxide makes up 95% of the lachrymator

And one final detail, most literature on the topic including this blog so far, discuss the lachrymator as if it’s a single compound. But  NMR analysis reveals it  to be a 19 to 1 mixture of (Z)- and (E)-propanethial S-oxide.

These are not earth-shattering revelations. But what was humbling is how the inaccuracies from a field that I know and enjoy almost got past me. Imagine what happens when I read news about economics and terrorism, stories that I often do not dig into to uncover the truth.