Sub-module 4D, Closure
Comments on Discussion about partitioning. The Level I model allows for three types of chemicals: Type I, which partitions everywhere; Type II which is involatile (does not partition into air); and Type III which is insoluble in water. I was hoping all your chemicals would fit into Type I, which they almost all did. If you are doing this again and have an insoluble or involatile chemical, try inputting it as a Type II or Type III. There is a help screen from the chemical input screen that explains this.
Most chemicals are soluble in water, to some extent. The word "insoluble" is therefore subjective, but useful, since many chemicals are insoluble for all practical purposes. If you see "insoluble" in one source, another source might give you the actual solubility. Many environmental contaminants are insoluble in one sense, but do in fact slowly enter the water. This may make them quite persistent.
Solubility is normally expressed as mg/L that is mg of chemical per liter of solution. If you see solubility expressed as a percentage, it may mean volume of contaminant per volume of water or mass of contaminant per mass of water, you'd have to dig to determine what they meant, but while you were digging you could find a source that has it in mg/L.
*** Often different sources in the secondary literature will have different values for the same constant. Log Kow for example. The herbicide 2,4-D (see http://www.24d.org/ for more on this chemical) has a log Kow listed from 1.57 to 4.88; that is over a thousand-fold difference. Those of you lucky enough to get to the Kow site, often found two numbers listed, an "experimental" number (or numbers) and a "Log Kow estimated number," based on an estimating technique. For example for cyclohexanol the experimental number is 1.23 and the estimated is 1.64. Often you find only one number in the secondary literature, but that is NOT a sure sign that the matter is definite, only that all the secondary literature writers used the same primary source. I have been horrified to follow up a secondary source back to the primary and find out that everyone has been using the same number from original research that was done in the 1920's and 1930's. That doesn't mean the old number was wrong, but it makes you wonder. On the other hand it is completely impractical to check these numbers yourself. One advantage with computer modeling is that you can easily do a sensitivity analysis by sticking in the highest and lowest values from the literature for the various constants into the model, and see if they are critical or not. We will do a little of this in a few weeks.
*** Q. In your example in 4A, you say that the ratio of octanol to water is
1000 to 1. If so wouldn't there be 55,000 mg/L in the fat tissue of fish if
55 mg/L dissolved in the water as opposed to 5,500 mg/l?
A. Excellent. No one else caught that.
***Q. In #7 it mentions "fictitious" authors, is this really a problem?
And
Regarding scientific journals and authorship. I worked on four separate research
projects; three of them as a paid laboratory assistant, and one of them was
my own (I was not paid). My name only went on the one project that I was not
paid for, and was my own research when it was published. I was told that since
I was paid, my name was not going on the papers. That seemed okay, but on the
flip side, other professors who did not do a lick of work on these projects
suddenly had their names plastered on all of the journal articles. What gives
here? I understand this is pretty common, but it sure does not seem ethical
from what I have read. What is the justification for this common practice?
Yes a big problem. Some "Institute Directors" get listed as author
on 20 or 30 publications per year. It is unlikely they significantly contributed
to the "research" on any of them. Essentially they have traded money,
lab space, or referrals, for authorship. That is 100% wrong.
*** In our discussion of literature, I forgot to mention some compendiums or standard reference books. These are not textbooks, in the sense they are used in a college course, but rather reference books in common use by similarly situated professionals. For example, (I'm not recommending you buy these, but looking around my book and paper strewn office): The Merck Index, has 3 or 4 paragraph descriptions of about 8000 chemicals in common use. Casarett and Doull's Toxicology has much basic and advanced information. NIOSH has its Pocket Guide to Chemical Hazards. The ACGIH produces the TLV booklet. There are others that I know folks use: Sax's Dangerous Properties of Industrial Materials is another commonly used book.
***Q. About the term paper; am I correct in reading that you want at least two references that are not from the internet? It seems that you are saying that you expect most of our references from the internet. I have never heavily relied on the internet for reference because it is usually considered an unreliable source. At most, I have used two, maybe three internet sources which I thought to be highly reputable and would not disappear in a few months as most web sites do.
A. You do not need to use any references from the Internet. I do expect you to do some web searching. The computerized library searching is accessed via the web, but the articles you are looking for are typically in paper.
*** Q. Since Octanol is as hydrophobic as animal tissue, I understand how it can be used as an indicator of which substances tend to enter animal tissue. The text states that substances with high Kow (above 2) tend to enter animal tissue. Was the number 2 derived from observation, or experimentation, or what? In my model, tetrachloroethylene has a Kow above 2, but a relatively small amount entered the fish. Can we assume that a higher Kow means that a comparatively higher amount of substance would enter the fish?
A. Yes, all other things being equal, the higher the Kow, the faster chemical will enter tissue from the environment. Some of the other things that might not be equal are volatility and solubility. Some chemicals will quickly enter the air, and then be swept away by wind and/or diffusion. Some chemicals are solid and remain in a lump, unless they are leached by rain. If they are insoluble, they do not leach, or do not go very far. At the cellular level, very large molecules do not enter the cells as fast as small molecules. Having said that, Kow is still a useful indicator and in common use.
*** Q. Speaking of water solubility…The model requires
input of both water solubility (g/m3) and log Kow….I am having
a difficult time with the difference between water solubility
and log Kow. Don't they both basically measure the same thing?
Will you ever have a chemical with both a high water solubility
and a high Log Kow? If they are directly related, why does the
model require both as input?
(and related question) This is more of a statement… I have
never heard lipophilic, non-polar, and hydrophobic used as synonyms.
They aren't really are they?
A. Put a liter of liquid chemical X and a liter of water in a two-liter jar, shake it, and let it stand for a while. When you come back, if there is only one layer, you say chemical X is "miscible." If you have two layers of about one liter each, you say chemical X is "hydrophobic." If you have two layers, but the layer with X is less than one liter, you say X is "soluble in water." You can describe this exactly, as 5.0 grams of X per 100 mL of water, implying that if you try to mix more than 5.0 grams with 100 mL of water the second layer will form, if you mix less than 5.0 there will not be a second layer. Often qualitative terms such as "poorly soluble" are used. Most hydrophobic substances are non-polar and most non-polar substances are hydrophobic, but the word "hydrophobic" is qualitative and hydrophobicity is relative. Both methanol (CH3OH) and octanol (C8H17OH) have the same polar character (how about "amount of polarity," hmmm.) in the OH or alcohol group. Octanol has a lot more non-polar character in the rest of the molecule than methanol, by an amount of 1:8 (roughly). So octanol is hydrophobic and non-polar (as a whole), methanol is both miscible with water and non-polar substances, like hydrocarbons. Likewise the word "lipophilic" is qualitative. The analysis of Kow is a method of measuring lipophilicity. But in general most non-polar substances tend to be hydrophobic, and have a high Kow and thus are lipophilic. No they are not synonyms.
*** Q. Although there I had completed my chemical simulation prior without too many problems with the log Kow website, I still had some issues. For one, in an attempt to find another website, I checked the MSDS sheets for the physical properties where the log Pow was listed. How is this related to logKow?
A. Some authors use "Pow" or just "P" where we use Kow. I am more familiar with the "K" usage.
**Q. Under Obligations of Reviewers (and editors) it mentions "Unpublished
information, arguments, or interpretations contained in a submitted manuscript".
What are they talking about? Don't manuscripts get submitted alone since they
will stand alone in publication?
A. Another big issue, sometimes. It means that the reviewers or editors cannot
"steal" the ideas they get from the unpublished document they are
reviewing.
**Q. What is an "evaluative" environment? Or do you mean evacuative?
A. That's Mackay's term for the model environment. He is trying to make sure
we understand that the model is only that, a model, not the real environment.
**Q. How is it determined if data is "falsified" or just poor science,
or random results? You always hear of researchers providing data that discredits
earlier research i.e. saccharine is not a carcinogenic etc. Does that mean somebody
lied? Does it mean somebody is not as good a researcher as they think? How do
you tell the difference?
A. Often it's a matter of reading the original research carefully, and not relying
on the secondary or tertiary literature for information. Often the scientist
reported exactly what he found; it was someone else that jumped to a conclusion.
Q. Doing Module4 I found a smart web source for chemicals. It even shows 3d structure of molecules! (Although it takes to download a small plug-in for either MS Explorer are Netscape Navigator) I got really excited about it. http://www.chemfinder.com/result.asp
A. Yes, a neat site indeed.