Science – Page 3 – Geeky Girl Engineer

Sampling Fish

Posted on May 26, 2015 by geek

Recently for work I got to help out in the field taking samples to quantify environmental contamination. Some of the samples we were taking were fish tissue to measure the levels of polychlorinated biphenyls (PCB) in them. The fish live in a river that was contaminated decades ago. The sampling results will be used for fish advisories and also to determine a clean up plan.

Sampling fish starts with the really fun part, which is cruising on a small electrofishing boat. Electroshocking the fish allows you to catch them alive and throw back any fish we didn’t want. We had target fish we were trying to catch to sample, and those were the only ones we kept, and we only the number of target fish we needed. The electroshock sort of stuns the fish but doesn’t kill them. The electrofishing boat has two long poles with anode wires hanging off of them protruding from the front of the boat. There were more wires hanging from the bow of the boat, and those are the cathodes. The electricity flows from the anodes to the cathodes. We stood at the front of the boat in rubber soled boots with nets extended waiting to catch any fish stunned by the electroshocking. Netting electroshocked fish is not actually as easy as it sounds. Some of the fish are more stunned than others, so some fish seem slightly confused but then swim away. Also, some were stunned but at a depth too low or cloudy for us to catch or see. According to the boat’s captain, the water had really low conductivity, which was making it difficult. Since we had target fish we were trying to catch, I, naturally, kept catching fish we didn’t want. I threw a lot of fish back. Still, a day on a boat catching or not catching fish was a wonderful change from the cubical I normally work in. Also, I learned that you really need polarized sunglasses when out on the water.

View from the boat with the anodes out in front. Not a bad office.

View from the boat with the anodes out in front and nets at the ready. Not a bad office.

Front of boat, cathode wires hang along bow

Anode hangs in front of the boat

Caught fish in boat’s holding tank

Once we got the fish to shore, the biologist took over. The fish were weighed and their length measured. He took a a sample of their scales from a standard location, and those scales were going to be used by a laboratory to determine their age. Evidently scales can be used to age fish in the same manner tree rings age trees. WARNING: If you are uncomfortable looking at the insides of fish, do not read any further. You should probably not eat fish also, if you can’t look at an uncooked one.

Scrapping scales off fish. Scales are used to age fish.

The rest of the scales were then scraped off. The fish were then cut. Only the fillets were used for sampling. The part of the fish used for sampling can differ depending on what the exposure pathway being examined is. We took two different parts: the filet, which represents what a human would normally eat, and also the fillet with rib meat. The rib meat is normally not eaten, but it would have more PCBs in it, so using it in the sample would represent a worse case scenario for a human consuming fish.

Cutting fish to take the samples

Fish samples ready for lab. Left side fillet also has rib meat. Right side fillet does not.

Fish post fillet and rib sample

Fish post fillet sample

I also learned a bit of fish anatomy during the sampling. The biologist was also sexing the fish.

Female brown bullhead fish with orange egg sack

Male fish with testes/seminiferous tubules indicated

We weren’t necropsying the fish, but we still got a look inside, including sometimes as to what it had eaten recently.

Fish gastro intestine tract. Eaten food is in stomach.

We sampled quite a few fish, but it was for science and to benefit the community.

Pile of fish that have had samples taken from them

It’s Not Melting, It’s Dissolving

Posted on January 16, 2015 by geek

Time for another post where I get on my science grammar soapbox. Have you ever seen the movie The Wizard of Oz? Everyone has seen that movie, right? Recall the scene where Dorothy throws a bucket of water on the Witch, and the Witch dissolves into a puddle while screaming “I’m melting, I’m melting”? First, don’t ever watch that movie with me. Why? Because every time I see that scene, I scream “you’re not melting, you’re dissolving, get it right.” Ok, it is a movie, a movie that takes place where monkeys fly, there are witches, lions walk and talk like humans, and scarecrows come to life. No, I shouldn’t be looking for realistic science in it. However it drives me crazy that they can’t even get the simple difference between dissolution and melting correct.

In the exact same incorrect way, there is a saying that some people say when their children, dog, whatever, is hesitate to go outside in the rain. “You are not made of sugar, you won’t melt.” There are actually several things wrong with that statement. Sugar, as in table sugar, which is specifically sucrose (as opposed to all the other sugars that exist), does not actual melt at all. At 186°C (367°F), it decomposes to caramel. So even if that saying meant decomposes, if the temperature outside is high enough for sugar to decompose, you have much bigger problems then possibly getting wet. You would die of heat. However, if you were made of sugar, and you went out into the rain, you would not have to worry about melting, you would have to worry about dissolving.

Melting is a physical process where solid turns into a liquid due to heat applied to it. Stick ice into a glass at room temperature. Wait a while. You now have water in the glass. The ice melted into water. But you didn’t apply heat, you might argue. The melting point of ice, the temperature at which solid water, i.e. ice, becomes liquid water is 0°C (32°F). So by simply having ice at room temperature (around 22 °C (72 °F)), heat has been applied to it. The temperature is higher than what the ice needs to stay a solid. Similarly put solid chocolate in a pot and heat slowly to 30°C (86°F). You have liquid chocolate. It has melted. Now don’t waste that chocolate, go eat it with strawberries or cake. [Excuse me for a moment. . .]

Now take that glass of water you made by melting ice at room temperature, and pour just a little salt into it. The salt has dissolved into the water. The water, which is the solvent, has dissolved the salt, the solute, into a solution. When Dorothy throws water on the Witch, the Witch is the solute, the water is the solvent again, and now you have a witch solution in water. Based on the film, witch dissolves quite readily. [It would not matter if she threw boiling water on the Witch, it would still be dissolution because the water is mixing with the witch. The water was quite clearly not boiling anyway.] Other liquids can act as solvents to dissolve solutes, but water is the most common in everyday life. Wiping acetone on nails painted with nail polish removes the polish because acetone, a solvent, dissolves the hardened nail polish, the solute, into a solution. [It is a temporary solution in the sense that acetone readily evaporates, but it forms a solution with the polish long enough to transfer the polish to a cotton ball. The acetone then evaporates leaving behind the polish on the cotton.] An important distinction between melting and dissolving is that melting only involves one substance, water, chocolate, wax, etc. Dissolution involves two substances, water and salt, water and sugar, acetone and nail polish, etc. Dissolution can also involve applied heat, but it isn’t required. There is a much longer explanation for that, and it relates to the solute and solvent and numerous other factors.

To review, melting is one substance changing from a solid to a liquid, and one, and only substance is involved. It is a phase change that must involve a temperature (or pressure) change. Dissolution is one substance becoming part of a solution with a liquid, and two substances are involved. It is two substances becoming one, and temperature change is not necessary for it to happen.

I honestly don’t understand why some people don’t understand the difference. However ignorance of this appears to be wide spread. Evidently the U.S. Special Inspector General for Afghanistan Reconstruction does not know the difference. That Inspector General recently released a report concerning a half-million-dollar U.S.-built police training center in Afghanistan that was so badly constructed that it is literally “melting.” Nope, it is not. It is literally dissolving. If the center had been made of wax, then maybe it might melt. Based on the wording in this article and the accompanying photos, the building is quite clearly dissolving. That is still incredibly appalling construction. As an engineer, I would really like to see the design plans. However, if the Inspector General does not even know the difference between melting and dissolving, then perhaps the Inspector General would do well to have someone on staff who does. It would make for better and more accurate reports.

WMATA L’Enfant Plaza Fire

Posted on January 13, 2015 by geek

Today there was a fire in a WMATA subway tunnel near L’Enfant. The National Transportation Safety Board (NTSB) is now investigating, and I have confidence that they will do a thorough investigation. I have some questions about actions taken right after the smoke was reported that no one, or at least no one in the media I have seen, has asked. The station filled with smoke, and they evacuated it. WMATA stopped running green and yellow trains through L’Enfant. However they kept running blue, orange, and silver trains through, but these trains did not stop at the station, as they normally would. For those not familiar with L’Enfant Plaza Metro Station, orange, blue, and silver lines share the same track on the lower level, and yellow and green share the same track on the upper level. My question is, were they sure it was safe to keep sending the orange, blue, and silver trains through? I am not asking from the standpoint of the fire, because presumably, they traced the location of the smoke enough to know it was not in the lower tunnel. By safe, I mean because of the potential inhalation of smoke in the lower level tunnels. If the station filled with enough smoke that it needed to be evacuated, then how were they sure that smoke would not enter the trains running through it?

A couple of quick points:

Just because air smells bad doesn’t necessarily mean it is toxic or hazardous, but conversely, just because air smells fine doesn’t mean it is safe.
Particulate matter in air and/or smoke is in general not something you really want to breath, but there are different levels of toxicity associated with it. That is, some particulate matter is not more than just an irritant. However, the effect particulate matter has on a person is also affected by that person’s health. People with respiratory issues are more susceptible to any effects.
Exposure to hazardous or toxic materials can cause effects on different time scales. People who were trapped on the WMATA train in the tunnel, would have acute (short-term) effects from breathing the smoke, such as coughing and having trouble breathing. However, they were probably also exposed to chemicals whose effect is not immediate, such as carcinogens.

The questions I have, that I have not heard anyone ask include:

What is the air exchange rate between the subway trains and the surrounding air? Can the ventilation be turned off manually, so that there was no air exchange between the train and the surrounding air while the trains were near L’Enfant?
Were there any measurements taken of the air in L’Enfant, particularly on the lower level where the orange, blue, and silver trains were still running through? If so, what were the measurements of? Just measuring particulate matter will not indicate almost nothing about organic compounds or other chemicals in the air.
How far did the smoke spread?
Assuming air measurements were taken, did anyone calculate the amount of contaminants that people in the trains would be exposed to while running through the station based on time and air exchange rate?

My educated guess is that no air measurements were taken. There are probably some sensors in place to measure smoke, but depending on how that measurement is taken, it will tell you information about the particulate matter and that is it. I seriously doubt there was initially any sensors that measured organic compounds or any other type of compounds in the air. I have my doubts that any portable system was put in place during the response. The priority would have been evacuating people (as it should have been). It is possible that WMATA had some qualitative data that there was not much smoke on the lower level. That is, someone may have looked at a video screen and decided the air didn’t look bad. However, unless they had actual quantitative data of what was in the air, then visual assessment of air is a really bad way to make assessments on the quality of the air.

The early statements by WMATA and all other sources, like the fire departments involved, was that they did not know the source of the fire, location or cause. Thus they could not have possibly known what was burning and what would be in the air. For example, if wood is burning, you can expect certain chemicals in the air. If rubber is burning, you can expect different chemicals in the air. WMATA probably decided that the air on the lower level didn’t look that bad, and the trains would go through the station quickly enough that very little exposure would occur. They very well may be right, but with no data and no statements about any calculations, they have no way to prove that. Also, did they inform their passengers of this? If I was on a train, and I knew that the train was going to go through, but not stop, at a station that was filling with smoke, I would get off the train. I don’t feel the need to expose myself unnecessarily to hazardous substances, even if in small amounts. I do not like standing near people who are smoking. The second hand smoke may only minimally increase my risk of disease, but I still don’t see the need for that tiny increase. Thus, was WMATA considering passengers’ exposures at all? Furthermore, did they communicate the possibility of exposure to their passengers on the orange/blue/silver lines to allow their passengers to make their own educated decision about staying on the train? My guess is the answer to both those questions is no, and that is another thing to which WMATA should be made to respond.

Collapse

Posted on January 10, 2015 by geek

One of the exhibits, we visited during Cultural Programs of the Natural Academy of Sciences’s #NAS_sciart was Brandon Ballengée: Collapse. Collapse is a huge pyramid of specimen jars that contain species from the Gulf of Mexico that are in decline due to the 2010 BP Deepwater Horizon oil spill. It was interesting to be able to see numerous species up close, even if preserved, that I normally would never see. However, it was sad to think that all these species are in decline or at least affected by the Deepwater Horizon oil spill.

Collapse

Crabs

Flouder

Giant sea roach

Octopus

Shells

Fish

Turtle

It’s Not Individualism or Bad Fashion, It’s Sexism

Posted on November 12, 2014 by geek

I once hypothesized that male heterosexual scientists and engineers single-handily keep the Hawaiian shirt industry in business. Don’t ask me why, but as a group, they love those shirts. I make jokes about their lack of fashion and just plain dressing ability. I tease because I love. I love their individualism, and I love how they don’t know or care about fashion. I may be a female heterosexual scientist and engineer, but I am one of them when it comes to dress. The last time I remember being fashionable was when I was in fifth grade. I don’t understand or like many fashions. I have my own style, and I like to look nice, but I consider my ability to wear jeans to work and not even own a suit, a serious perk of my career (and employer).

And then there is this.

No no women are toooootally welcome in our community, just ask the dude in this shirt. https://t.co/r88QRzsqAm pic.twitter.com/XmhHKrNaq5

— Rose Eveleth (@roseveleth) November 12, 2014

This is Rosetta Project Scientist Matt Taylor of the European Space Agency (ESA) in a shirt covered in scantily clad women in in sexually suggestive poses. That is the shirt he chose to wear on a day when ESA did the amazing feat of landing a probe on a comet. This is the shirt he chose to wear on a day when he would be interviewed by the media and featured on live webcasts of the events. Not only did he not see a problem with this shirt, but evidently no one else at ESA did either. This. Is. Not. Acceptable. This is not appropriate. This is offensive. This shirt should not exist period, but it most certainly should not exist in the workplace. This is not about how ugly the shirt is. This is not about how unprofessional a shirt like that is. This is not about Dr. Taylor being an individual and expressing his style. This is about a shirt that objectifies women. This is about a shirt that is sexual harassment without Dr. Taylor even opening his mouth or making any type of gesture or doing absolutely anything other than wearing it. This is about a complete and utter lack of respect of women on the part of Dr. Taylor and evidently everybody at ESA who works with him and would have been in a position to say something. This about no one over there seeming to care about whether or not women feel comfortable working there when someone can wear a shirt like that. This about telling women it doesn’t matter your intelligence, skills, education, or ideas, you are but sex objects. The STEM fields continue to have a problem with sexism and gender inequality. My alma mater, a technical college, still only has about a 25% female student body. Wearing shirts like that to workplace will not help. It will not tell women that they are welcome. I quite frankly don’t care if Dr. Taylor is actually a really nice guy who is actually very supportive of women in STEM. His shirt says otherwise. He and ESA owe all of us an apology. That shirt overshadowed what should have been the main headline that ESA did the absolutely spectacular task of landing a probe on a comet. That shirt and the attitude it expressed ruined it for me in fact.

Finally, I would like to give mad props to Dr. Paul Coxon for his absolutely awesome idea, that if you want to wear a shirt with women on it, wear one with these women on it.

Awesome idea! RT @paulcoxon: @edyong209 @MCeeP @Mammals_Suck I’d wear a shirt with *these* women on: pic.twitter.com/egyu55QzpS

— Geeky Girl Engineer (@gkygirlengineer) November 12, 2014

These would be some of the women of the Indian Space Research Organisation (ISRO) celebrating after ISRO’s Mars Orbiter Spacecraft successfully entered the Mars orbit. And they are awesome.

Do not mess with a toxicologist

Posted on October 28, 2014 by geek

I was attending a lecture today on toxicology, and of course the subject people purposely poisoning other people came up. The lecture relayed the story of a female chemist who had a romantic relationship with a male chemist who worked in the same lab. The male then broke off the relationship and starting dating another female chemist who also worked in that same lab. The first female chemist evidently pretended like she was ok with everything and continued to make tea for everyone afterwards. However she started adding acrylamide to the male’s tea. It sounded like the poisoning was discovered fairly quickly. He then relayed another story of similar circumstances when a male broke off a relationship with another woman, but they continued to work together. She used thallium to poison his tea. She however was a toxicologist and made detailed notes of the effects on the male. She then adjusted the dosage accordingly. My lecturer did not relay information as to when she was caught. Summary of the story is don’t piss off a toxicologist, and if you do, don’t be stupid enough to let the person make your tea.

DISCLAIMER: This is in no way meant to encourage people to poison people. Don’t do that. Seriously, don’t.

Old Medical Journal Memos

Posted on September 25, 2014 by geek

I have a confession. Sometimes I am not productive as I should be because my curiosity gets the better of me. I need to look something up, and in the course of researching it, I read some other tangental tidbit, which cause me to look something else up, and then down the rabbit hole I go. Case in point was today. I have a project at work that involves a database of environmental contaminants. The short version is, these contaminants are in the database under numerous synonyms, including synonyms that are insanely obscure and uncommon, or perhaps they were common a hundred years ago, but certainly not today. All the contaminants are in the database associated with their CAS Registry Numbers, so it is clear what the chemical is. [A CAS Registry Number is like a Social Security number for a chemical. It is specific to a chemical or a specific type of mixture of chemicals.] Many of these synonyms I have never heard of before. One synonym for nitrobenzene was oil of mirbane. I had to look this one up for pure curiosity reasons. After much searching, I have yet to find out the etymology of oil of mirbane or simply the word mirbane. [@vonOberst on Twitter suggested thusly “Mirer is a candle in French. Bane is “fatal”…maybe someone tried to make a candly from nitrobenze crystals?” For the non-chemists, nitrobenzene is among other things, explosive, so a candle made from it would definitely be a fatal candle, and I find this idea disturbing and amazing. If anyone knows the etymology I would seriously love to know from where this name came.]

Anyway, in the course of searching for the origins of oil of mirbane, I came across a British Medical Journal memoranda from Jan 27, 1912 (1(2665): 183) about someone who was accidentally poisoned with it. The article didn’t get me to a better understanding of that name, but it was an interesting article, and I became interested in these old memoranda and the way they were written, diagnosis, and treatment. So then I had to read a few more in this volume, and now reading old medical journal memoranda is going to become my new hobby. They are fascinating. However, I need to share part of my favorite one from that volume, “A supposed case of heat-stroke: remarkable recovery.” This report is completely fascinating, and I would really love to know from what this patient was suffering. I have no medical training, but this does not sound like heat stroke as it has been described to me in first aid training. The case as described.

“A man, aged 53, was crossing a road during one of the hottest days of last summer, when he suddenly found himself on the ground, with a “horse’s hoof right on top of him”; this was his description of what happened. He picked himself up and ran across the road to his son, who was waiting for him on the pavement, and who brushed the dust off his clothes.He complained of no pain or discomfort of any kind, but his son took him into a chemist’s shop, where he was given a dose of sal-volatile. He then went home by train (a distance of eight miles), sat down and made a good tea, feeling quite well all the time. Towards the end of this meal he became a “little queer,” went upstairs and felt very ill indeed, and remembered nothing afterwards. This attack came on about five hours after he had fallen down in the road.”

Read the whole article. It is not long and is truly fascinating. Included is the information that the doctor examined him and found no injury, which kind of calls into the question the idea of a horse hoof on him. I am not sure what I love the most about this article, but the pure Britishness of it is definitely part of it. I adore the details that the son helped brush dust off the man, which makes me wonder what the son was doing when the man fell down in the road or whatever he did. Also, of course the man went home and made a good tea. The man recovered after his attack over the three days, then he got worse. Part of the treatment that was given to him when he fell unconscious was withdrawal of cerebrospinal fluid. It never states why. The patient got better after that, then got worse, then they removed more cerebrospinal fluid, and he got better again. Evidently his “heat stroke” was cured by removing cerebrospinal fluid. Is this still something done for heat stroke? How exactly does removing cerebrospinal fluid help heat stroke or anything? I actually would like to know why this was done, or what the theory was back then (or now?!).

Thus now, I reading these old medical memoranda is going to be my new thing during my free time. The article before the heat stroke memoranda describes two children suffering from tetanus infections who were treated unsuccessfully with magnesium sulfate injected into their cerebrospinal fluid. One of the children was also given strychnine. This makes me all the more thankful for tetanus vaccines, even if they do hurt.

NMNH Cetacean Collection

Posted on August 25, 2014 by geek

Friday I got the incredible opportunity to take a behind the scenes tour of Smithsonian Institute’s National Museum of Natural History. They let a small group of people take a tour of the cetacean collection stored in an offsite location. NMNH has the largest marine mammal collection in the world, and it is awesome. [More properly said, the people of the USA have this amazing collection, and NMNH has been endowed to take care of it.] Most of their specimens are not on display to the public but are stored offsite and in a manner where they can easily be studied. Charley Potter and Nick Pyenson, scientists at NMNH, showed us many of the cetacean specimens, talked about what they do, and answered our questions. I want to thank NMNH and their staff, especially Hilary-Morgan Watt, Katie Sabella, and Trish Mace, for letting us take this amazing tour. Also, thank you to Steve Thornton, a visiting researcher, who gave us a detailed description of how dolphins use their nasal passages to make noises, which at least in my humble opinion is fascinatingly and amazingly complicated. Also, I would like to thank them for having their specimen collection online. I missed some of the species names of specimens we looked at, but because the specimen number was visible in some of my photos, I was able to look up information about the specimen through their website. This is an incredible resource.

They had two bottlenose dolphin skulls out sitting side by side. One was from a coastal bottlenose dolphin, and one was from an offshore one. When sitting side by side, it was easy to see how much smaller the coastal one was than the offshore one. The morphological differences relate to their different eating habits, as the offshore ones feed on larger animals.

Bottlenose dolphin skulls, on left is coastal one, on right is offshore one

Coastal bottlenose dolphin skull

They had part of a forelimb bone from a right whale. The fungal like growth on it was bone that had grown around something on which it had been entangled.

Right whale forelimb bone with entanglement growth

Right whale forelimb bone with entanglement growth (zoomed in)

There was a drawer filled with narwhal tusks. Only males have the tusks, and most twist in the same direction. Most have a polished end. Up close they really pretty and have interesting texturing. They are hollow with varying diameters.

Narwhal tusks

Narwhal tusk

In the same cabinet as the narwhal tusks are pieces of baleen. Baleen can be used to distinguish different types of whales and is fast growing like hair. Examining the baleen can give information about the trophic feeding level of the whale and can give up to 40 years worth of information on the whale and water conditions, by analyzing it along different points along its length. Before plastics and fiberglass was invented, baleen was split into rods and used in such things as umbrella skeletons, of which they have one.

Baleen, Charley Potter is holding one piece. In box in drawer is an umbrella skeleton made from baleen.

Baleen

Baleen, zoomed into hairy edge

They have an amazing collection of skulls. There are skulls upon skulls filling up shelves. The skulls are placed side by side by species and thus can compared easily. There were numerous Baird’s beaked whale skulls that had various shades of white and off white depending on the conditions in which they were found.

Baird’s beaked whale skulls

Baird’s beaked whale skull

Baird’s beaked whale skull, zoomed in

The Blainville’s beaked whale skulls were really interesting. The males have two giant, erupted, modified teeth on their jaw, which are used for combat. The beaked whale skulls are the only skulls which can be sexed. The males have very dense skulls and thus are quite heavy when compared to the female skulls that were approximately the same size. They let us life each one by the beak, and the difference was really obvious.

Blainville’s beaked whale skulls, female on left, male on right

Blainville’s beaked whale jaw

Male Blainville’s beaked whale teeth

They were still processing some specimens. There was a pilot whale skull out that had a lot dried soft tissue attached to it.

Pilot whale skull

Pilot whale skull, zoomed in on soft tissue

There was another skull sitting next to the pilot whale skull that was some type of beaked whale. I was completely fascinated by the porousness of the bone.

Beaked whale skull

Beaked whale skull, zoomed in

There was also a bag full of vertebrae. I don’t know what species it was from, but the pattern on the vertebrae was really interesting.

vertebrae

In an adjoining building they had the bones from the really large whales. The building was complete with a giant garage type door through which to bring the specimens. There were shelves filled entire vertebral columns from various whales. On the floor was the skeleton of a right whale.

Right whale bones

All the skulls were propped up on metal carts. They were placed vertical for easy study. Because of the way a Sei whale skull was placed vertical, the radiating lines on the palette could be easily seen. All baleen whales have these lines, and the lines house blood vessels and nerves that feed the baleen.

Sei whale skull

Sei whale skull baleen marks

There were several gray whale skulls all sitting next to each other. The skulls were collected from various years and includes one from pre-1850s. The genetic makeup of the whales before and after the whaling industry can be compared, and it will give information about the genetic bottleneck that occurred due to whaling and the diminished population.

Gray whale skulls

They also had a blue whale jaw bone that is not only the largest blue whale jaw bone ever collected, it is also the largest single bone ever collected from any creature that has lived on Earth.

Blue whale jaw bone

Finally there was a North Atlantic blue whale skull, which was just amazing to view. It completed dwarfed us when we gathered for a group photo in front of it.

North Atlantic blue whale skull

#SIWhales participants with the North Atlantic blue whale skull

SAS Macro to Validate CAS Registry Numbers

Posted on June 25, 2014 by geek

*updated 7/20/15 after finding more ways people write CASRN or create fake CASRN that will sneak through my original macro*

I wrote a simple and fairly short SAS macro to validate CAS Registry Numbers. I have gotten enough free SAS advice and a few macros from various internet sources, so I thought it only fair to share this if it of use to anyone. Hopefully the comments give ample information about what input is needed and what the output is. The macro will catch an invalid CAS RN if it is

too long
too short
has all 0’s
does not return the correct check digit based on CAS calculation

Information about proper CAS RNs can be found from ACS who produce CAS RNs. Contact me if you have questions about the macro or find an error with it.

*macro to determine if a CAS number is a valid CAS number;
*input is name of dataset to be examined where CAS numbers have variable name CAS_number;
*returns valid = 1 if CAS is valid and valid = 0 if invalid CAS;
*returns character variable CAS which will be CAS number with hyphens and no leading 0s;
%macro CASnumber_check(CAS_dataset);
data &CAS_dataset (drop = CAS_num CASlength R N1-N9 QR Q Rcheck j);
length CAS_num $ 10;
set &CAS_dataset;
*give CAS numbers with alphabet characters or that are blank a 00-00 CAS number;
if CAS_number = “” then CAS_number = “00-00”;
if anyalpha(CAS_number) ne 0 then CAS_number = “00-00”;
*determine if CAS is numeric or character variable;
CAS_vartype = vtype(CAS_number);
*if CAS is numeric, converts it to character;
if CAS_vartype = “N” then CAS_num = STRIP(PUT(CAS_number, 8.));
*if CAS is character, removes all non-numeric characters;
if CAS_vartype = “C” then CAS_num = compress(CAS_number,,”kd”);
*breaks CAS number apart into digits;
CASlength = length(CAS_num);
R = input(substr(CAS_num,length(CAS_num)),8.);
QR = 0;
array N_(9) N1 – N9;
do j = 1 to 9;
if CASlength > j then N_(j) = input(substr(CAS_num,CASlength-j,1),8.);
else N_(j) = 0;
QR = QR + N_(j)*j;
end;
Q = int(QR/10);
Rcheck = QR – Q*10;
*checks on validity of CAS based on check digit and length;
if Rcheck = R then valid = 1; else valid = 0;
if N9 = 0
then if N8 = 0
then if N7 = 0
then if N6 = 0
then if N5 = 0
then if N4 = 0 then valid = 0;
if CASlength < 5 then valid = 0;
if CASlength > 10 then valid = 0;
*builds character variable called CAS with no leading 0s;
if N9 ~= 0 then CAS = cats(N9,N8,N7,N6,N5,N4,N3,”-“,N2,N1,”-“,R);
else if N8 ~= 0 then CAS = cats(N8,N7,N6,N5,N4,N3,”-“,N2,N1,”-“,R);
else if N7 ~= 0 then CAS = cats(N7,N6,N5,N4,N3,”-“,N2,N1,”-“,R);
else if N6 ~= 0 then CAS = cats(N6,N5,N4,N3,”-“,N2,N1,”-“,R);
else if N5 ~= 0 then CAS = cats(N5,N4,N3,”-“,N2,N1,”-“,R);
else CAS = cats(N4,N3,”-“,N2,N1,”-“,R);
run;
%mend CASnumber_check;

Formaldehyde in Baby Shampoo: Cancer or Sensitivity Issue?

Posted on March 14, 2014 by geek

An article was recently published in Slate about Johnson & Johnson reformulating its baby shampoo to remove formaldehyde. The article discussed how some people’s somewhat misguided fears about a known carcinogen, formaldehyde, caused its removal from baby shampoo, when in reality if you are worried about carcinogenic exposure to formaldehyde, baby shampoo should be the least of your concern. As the article’s author, Tara Haelle, correctly points out, formaldehyde is a naturally occurring substance. It is produced in normal atmospheric reactions and when wood burns, both during natural forest fires and human caused fires. It is also produced during anthropogenic activity from numerous industrial processes and petroleum fueled combustion, i.e. cars, ships, airplanes (Salthammer et at. 2010).

I have a few issues with this article, however. First, it states “high enough doses of inhaled formaldehyde can cause cancer, leading OSHA and the EPA to set limits for safe exposures.” Second, it quotes two chemists who say in different ways that the toxicity of a chemical is related to its dose or the amount of exposure, and it essentially states that formaldehyde only causes cancer in high doses. Finally, it completely fails to mention another reason why formaldehyde may have been removed that has nothing to do with cancer.

The problem I have with the second point, is that formaldehyde is a carcinogen, and the toxicological theory with carcinogens, is that exposure to one molecule of a carcinogen can theoretically cause cancer, depending on the carcinogen’s mode of action. With non-carcinogens, it is appropriate and scientifically accurate to say that the dose makes the poison. There are substances that to be healthy you need in some dose, but exposure to too high of doses can lead to detrimental health effects, for example iron and a whole bunch of metals. There are others that you don’t need at all, but you can be exposed to a certain dosage with no ill effects. However, with carcinogens depending on the mode of action for the carcinogenicity, it is believed that there is no safe level of exposure. In theory, all it takes is one molecule to cause a cell to multiply out of control and cause cancer. This is where the carcinogenic mode of action is important. The carcinogenic mode of action refers to how a particular carcinogen actually causes cancer to be initiated. If, for example, a carcinogen’s mode of action is mutagenicity, like radiation, then exposure of any dose can potentially cause the effect that leads to cancer. Thus, there is considered to be absolutely no safe level of exposure to that carcinogen. Each additional exposure increases your risk of getting cancer. However, there are other carcinogenic modes of action, and carcinogens with certain other modes of action would be considered to have a exposure threshold below which no cancer would occur.

So what about formaldehyde? What is its mode of action for carcinogenicity? Is there a safe level of exposure below which there is no risk of cancer? In the US, that appears to be in debate. This brings me to my next point. It is misleading, and in my opinion just plain legally and scientifically incorrect, to state that OSHA and EPA set limits for safe levels of exposure. The EPA has calculated formaldehyde’s Inhalation Unit Risk (IUR) for cancer to be 1.3 x10^-5 per µg/m³. “EPA estimates that, if an individual were to continuously breathe air containing formaldehyde at an average of 0.08 µg/m3 (8.0 x 10-5 mg/m3) over his or her entire lifetime, that person would theoretically have no more than a one-in-a-million increased chance of developing cancer as a direct result of breathing air containing this chemical.” The word “increased” is important. It means that it is already assumed that there will be a certain number of cancer cases, and this concentration would cause additional cases above background. Furthermore, EPA states that for calculation of cancer risk from formaldehyde exposure, a linear approach with a multistage procedure due to additional risk at higher concentrations should be used. A linear approach means that any exposure causes a cancer risk with each exposure increasing the risk, and the multistage procedure means that high concentration exposure causes risk to increase at a greater rate. A linear approach is the more conservative method with carcinogens and is normally used when there is not enough scientific evidence to devise a threshold or a different risk method. With that being said, EPA is currently reviewing its toxicity assessment for formaldehyde, and it is possible when that assessment if finalized, EPA will change it cancer risk approach. With respect to OSHA, they have set an permissible exposure limit (PEL) at 0.75 parts formaldehyde per million parts of air (ppm) as an 8-hour time weighted average. The reasoning behind this level is complex, but in part, they state “this PEL represents OSHA’s best judgment of the exposure limit, along with the ancillary provisions, necessary to eliminate a significant risk of harm to employees.” The phrase “significant risk” is in there because their calculations, like the EPA’s, involve uncertainty and probabilities. They are not stating that below the PEL there is no risk, it is just not as significant. Neither OSHA or EPA is stating that below some level of exposure, formaldehyde will not give you cancer. They are stating it unlikely or insignificant compared to a background cancer risk. Below the set levels, the risks are really low, but they still exist.

Back to the baby shampoo. I do, in fact, agree with the point of the article that formaldehyde in baby shampoo is not a concern for cancer. However, I would not state it will not cause cancer. I would state that possible formaldehyde exposure in baby shampoo is highly unlikely to cause cancer. An additional point, which is not in the article, is that formaldehyde is not readily absorbed through the skin, and the amount of volatilization of formaldehyde, which could then be inhaled, from baby shampoo is likely to negligible.

With all that being said, I don’t necessarily agree that removal of formaldehyde from baby shampoo is a case of chemophobia and an overblown reaction by a company. It is possible that Johnson & Johnson removed formaldehyde not because of cancer concerns but because formaldehyde is a known sensitizer and allergen. Many skin care products contain formaldehyde or formaldehyde-releasing preservatives, which include quaternium-15, diazolidinyl urea, DMDM hydantoin, imidazolidinyl urea, bronopol, and tris nitro. While only a small percentage of people have a sensitivity or allergy to formaldehyde, for those that do, it is safest to avoid any exposure. Whether or not baby shampoo containing formaldehyde could cause a person to actually develop a sensitivity or allergy is another subject.

I have no idea why Johnson & Johnson actually decided to remove formaldehyde from baby shampoo, other than that it was a business decision. However by removing formaldehyde, regardless of any cancer concerns, there is now a small but real percentage of potential consumers who can buy their baby shampoo without concern of skin reactions due to their formaldehyde sensitivity or allergy. Thus assuming there is another safer preservative that can be used in place of formaldehyde, its removal would seem, to me at least, to be a good business decision, as they have increased their customer base to people with certain skin sensitivity and allergies.