Tuesday, June 30, 2009

The Credibility of Science

As happy as I was with the Melendez-Dias decision, I am also bothered by some longer term implications for science, namely its credibility.

Being a scientist, I am fully aware of all its flaws and shortcomings. I know what they are and how to best deal with them. The general public is not. The most common perception, which is desirable to me, is that they look upon science as providing factual answers that are generally not be questioned. With every passing scandal however, this perception fades. The decision mentioned above adds to this. While I certainly have no problem with people understanding that science is not perfect, the attitude that is arising seems to be that science is just an opinion, and since it is an opinion, anyone can hold their own and they are all equally valid. (This is analogous to the people that downplay evolutionary theory by stating it is "just a theory", although that argument is fatally flawed for reasons that I won't get into here.)

"Voting" in science certainly doesn't help, such as when the IAU voted that Pluto was not a planet or when 1500 scientists formed a 'consensus' opinion on global warming. This continues to give the general public the perception that science is an opinion.

Add to that the endless "health" stories about how eating ___________(insert the food the day here) is prevents __________________ (insert the illness of the day here) only to be contradicted by a report next week that the same food actually causes that same disease and you have the makings of a immensely poor perception of that factuality of science.

I'm not sure what can be done. Education is desirable, but won't work. Newly minted scientists have a very poor understanding of the inner workings of science including the flaws that I alluded to above. It takes more than a few years to really see the true picture - some never do. There is no way we can expect better of the general public given that most of them thought their science classes were dreadful.

I wish I could think of something.

We don't do logos

I often accompany our sales people on initial sales calls. Explaining what our company does is somewhat difficult, a challenge that I will leave for another post, but clearly we work in most areas of materials science. What I really enjoy is when the clients ask what we don’t do. If the atmosphere is light enough and I’m quick enough, I can interject: “We don’t do logos”. It always gets a good laugh.

Certainly we needed a new logo a few years ago, as our previous logo was clearly dated.
Can anyone guess what that large central section of the leaf is a portion of? (Answer at the bottom of this post). Hint: you need to be at least 30 years old or if not that, had access to a computer that’s at least 15 years or so. I don’t know why that was part of the logo, as we certainly didn’t develop computer software either.

We can’t do anything that looks like an aspen leaf, as the Aspen Medical Group in town already has a logo like that and our lawyer just doesn’t want to go anywhere close to that.
Being no longer closely linked with any piece of human construction, our new logo clearly will not become dated as technology advances, but we (i.e., most of my colleagues) still don’t like it. It’s not that we’re opposed to pentavalent compounds, as they clearly exist: PF5 and ClF5 to name a couple. It’s just the cartoonish nature of the logo, the green and the black, the distorted perspective. One former manager called it a squished turtle.

Answer: it’s part of a 5 ¼” floppy drive.

Friday, June 26, 2009

Melendez-Dias v. Massachusetts - More Commentary

The Melendez-Dias v. Massachusetts case was decided. The heart of the issue before the Supreme Court was that whether or not the defendant had the right to cross-examine the analyst who had prepared a report identifying some drugs. The Sixth amendment states that defendant have the right to cross-examine their accusers. The issue was whether or not the report, and thereby the analyst was an accuser. The Court, by a 5-4 margin decided that indeed the analyst can be cross-examined in court. (It was an unusual split, with Scalia writing the decision and joined by Thomas, Stevens, Souter(!) and Ginsberg (!!))

My (non-legal) opinion of the matter is that being a chemist, I am too well aware that scientific measurements are not the objective and neutral procedure that nonscientific people think them to be. The neutrality is somewhat harder to argue against, but arguing against objectiveness is much easier. There are simply too many things that can go wrong with modern instrumentation to not question there results. I do that everyday here at Aspen Research. Not that we do poor work, but the question always arises “What are we really measuring?” Answering this makes our work that much better for the clients we serve. And as I’ve pointed our before, there is a huge gap between data and conclusion, one that requires human intervention. Given all of this, I do think there is sufficient doubt on any analytical test report that it should not just be taken as a matter of fact.

Many documents used as evidence in court are clearly not accusatory and that should not change. The most common example is bookkeeping records used in accounting cases. The difference here is that the bookkeeping records do not reach a conclusion – both sides are able to argue the evidence to support whatever conclusion they desire. In contrast, a lab report has already reached a conclusion,

I love reading Scalia's opinions as he has no problem with directly addressing what specifically is written in the dissenting opinion. (He was particularly vitriolic when he wrote the opinion on the recent 2nd amendment case.) This one wasn’t quite as pointed, but there are a few gems such as this:

“Dispensing with confrontation because testimony is obviously reliable is akin to dispensing with jury trial because a defendant is obviously guilty. This is not what the Sixth Amendment prescribes.” (page 12)

This comment from page 14 particularly struck me hard:

“This case is illustrative. The affidavits submitted by the analysts contained only the bare-bones statement that “[t]he substance was found to contain: Cocaine.”... At the time of trial, petitioner did not know what tests the analysts performed, whether those tests were routine, and whether interpreting their results required the exercise of judgment or the use of skills that the analysts may not have possessed. While we still do not know the precise tests used by the analysts, we are told that the laboratories use “methodology recommended by the Scientific Working Group for the Analysis of Seized Drugs…At least some of that methodology requires the exercise of judgment and presents a risk of error that might be explored on cross-examination.”

A one line report with no basis for reaching the conclusion? Unbelievable.

My argument above is based on issues in the real world, but at least restrained by pursuing the “truth”. However, real world practicalities that do show up on page 20 are maddening:

”Perhaps the best indication that the sky will not fall after today’s decision is that it has not done so already. Many States have already adopted the constitutional rule we announce today, while many others permit the defendant to assert (or forfeit by silence) his Confrontation Clause right after receiving notice of the prosecution’s intent to use a forensic analyst’s report… Despite these widespread practices, there is no evidence that the criminal justice system has ground to a halt in the States that, one way or another, empower a defendant to insist upon the analyst’s appearance at trial.”

The dissenting opinion is loaded with even more “real world” practicalities. Since when do these matter in a legal decision on the Bill-of-Rights? All of the Bill-of-Rights makes life more difficult for the government. That should never be an issue.

I’m happy for this decision, as I think it is a right one, but that it wasn’t made for all the right reasons. There is that old saying that “Law are like sausages; people should not see them being made”, which I always thought applied to the legislative process. Now I see that it can apply to the judicial process as well.

Thursday, June 25, 2009

Melendez-Dias v. Massachusetts is overturned

A decision was finally reached, and it does appear that a written lab report is considered "testimonial" evidence, so that the person preparing can be brought to court to be questioned.

I'm short on time today, but will write more tomorrow. I agree with the decision, but am disappointed that it was only 5-4. Dissent is good, but this is too close for comfort.

Formulations, insomnia and career paths

I'm finally getting to work on that UV-cured material after endless delays from the front office. It is a new area that doesn't seem to have any previous work done, so I'm flying by the seat of my pants, using only my intuition and experience. This is no time for a designed formulation scheme spit out blindly by a canned program devised by a mathematician (or worse yet, a statistician!). This is the time to take big broad swatches of color and go for it, guaranteeing equally big failures and maybe, just maybe, a spark of success that can be slowly fanned and improved to reach the ultimate success.

The first days are the worst as there are too many functional groups to look at (including the various remnants binding them together), too many photoinitiators, and too many other additives to include. My mind was non-functional yesterday after massing out all the ingredients. Letting things sit overnight, I can already see that there are issues of solubility between the components to address, premature reactions and a host of other problems to solve.

This is fun. These problems will keep me awake at night, but I'm energized in the morning about the new ideas to try. Had I'd gone to the dark side (management), I'd be awake at night too with problems in my head, but that would be a worry-induced insomnia, the kind that would leave me exhausted in the morning from a sleepless night. I've chosen my career path correctly.

Tuesday, June 23, 2009

If anybody dares quote Paul Simon...

...I'll instantly delete their comment. It's just too easy a target, given that Kodak is stopping production of Kodachrome.

I certainly appreciate digital photography - I wish I would have had it around when I was learning the art. It's so much easier to show someone the benefit of bracketing exposures (i.e., taking a series at different shutter speeds or f-stops so as to get a better picture than what the dummy automatic settings choose) as you get instant feedback at virtually no cost. And it's so easy to delete the bad exposures instantly to not fill up the memory.

Using film in the same manner was a time-extensive and expensive. Even if you developed the film yourself, it still was a good hour or more between pressing the shutter and looking at the proofs. It also explains why skilled photographers were happy to get 2 good shots from a roll of film. But because of the irreversible nature of film, all the shots had to be developed.

I've also always been impressed with the technology of photography, particularly color. Being a chemist, I understand the technology, but I still am awed that this was created decades ago. It's a pretty precise technology and it performs beautifully.

Monday, June 22, 2009

It's finally time for bifocals

I've been fighting it too long, but this will most likely put me over the edge: The ACS is now rotating and condensing it's journals. The rotate I can maybe live with. Certainly it may appear at a distant that I would be looking at a solicitous image ("getta load of those hydrocarbons"), but that's o.k. It's the "condensing" that will cause me to concede defeat.

I certainly understand the move, although I had to smile at this comment in the announcement: "At ACS, demand for our print-based offerings has declined significantly—down over 50% in the last 2 years. Ironically, despite pre-emptive moves to digital presses, this has had the impact of increasing ACS’ own print-cost per copy, given the economies of scale in printing process." I'm sure other publishers will follow as well.

A transition to online is inevitable for all these publications. The issue I find with online access is that it is only temporary access, and when the fees are no longer paid, all access is lost even during the periods when full access was available. Meanwhile printed journals are permanent.

Friday, June 19, 2009

Buckyball polymers

This one has me a little bit puzzled in a number of ways. A paper at the physics arxiv discusses the polymerization of buckyballs (fullerenes)using 1,2,4-trimethyl benzene (TMB) as a comonomer. The resulting polymer then was an alternating copolymer.

From page 9:"However, the solubility of the material was found to change with time. Unlike raw C60 powder, well known to be highly soluble in aromatic solvents, the as-made nanowires were only partially soluble in these solvents, and this solubility decreased further with time." This is doubly puzzling, not only because of the change over time in solubility, but also because I would expect the TMB to have only a minor change on the over interactions between solute and solvent. There are 60/9 more carbon-solvent interactions with the buckyballs than with the bridge.

All of the easy explanations are not available: "We noted that the resulting nanowires were highly stable, as indicated by the fact that there was no detectable alteration in either their crystalline morphology, crystal color, or sample weight as a function of time." It's problem that will have to wait for someone else to solve.

Wednesday, June 17, 2009

At least here the Editor loses his job

Following up on last week's post about the nonsensical research article that was accepted in an open access journal after being "peer-reviewed", the editor of the journal has resigned his position.

What really gets me is the gaul of the publisher to state "In a statement, Mahmood Alam, director of publications at Bentham Science Publishing, told Nature in an e-mail that "submission of fake manuscripts is a totally unethical activity and must be condemned.""

But it appears that I am too quick to judge. Alam was actually the good guy here, actively purusing the criminals: "Alam claims that those behind the fake paper "had also tried to do this earlier [sic] in a different journal, but failed in their attempt due to our peer review system. Our suspicions were aroused this time and in an effort to unmask their identities the normal publication process was carried out on the second fake article. When they received repeated requests from us for more information and their credit card and other payment details they withdrew this paper.""

Way to go! A publisher trying to out the fakes, tracking them by their credit cards numbers. Too bad that the general public doesn't know about this stuff; I'd love to see the talk show hosts get some mileage out of this situation (and Conan needs a lot of mileage).

Tuesday, June 16, 2009

A sign of economic turnaround?

Being the economic forecaster par excellence that I am, please be assured that you can invest your entire life savings on the following sign of the imminent economic turnaround: next year's K-show is already sold out. This years NPE has been hurting in every possible way - attendance by both exhibitors and attendees is off.

The K-show is the Kunststoff show which is held every three years, Kunststoff being the German world for plastics. I used to think that "Kunststoff" was an inferior word to use, as the origin of "plastic" to describe polymers arose from the plastic deformation that they commonly underwent. But given that most people aren't aware of what "plastic deformation" is (i.e., they think that any deformation (including an elastic strain) of a plastic is a plastic deformation), maybe it is a better term after all.

Friday, June 12, 2009

Front row seat to a horse race

Just in my RSS feeds, I ran across two papers (1, 2) that made me think "deja vu" until I realized that no, these were two nearly identical papers. Both were using azobenzene derivatives, which have been known for decades to undergo a reversible cis/trans transformation under UV light, and both groups have now been able to demonstrate reversible bending of thin polymer films as a result of this. The first paper listed above was done by the Koshima group at Ehime University, while the second above was done by researchers at in the Yu group at Fudan University and others at the Tokyo Institute of Technology. Both groups have videos of the results. The JACS publication was received December 22 of last year, while the other paper was received March 11 of this year. That doesn't really clarify who was the originator though. Lastly, the JACS paper does cite earlier work of the Chinese, but the Chinese don't mention the work of the other group.

Coincidence? Academic spying? Is Hollywood calling for the movie rights?

Guar Gum - It's not just a thickener anymore

This research has it all: ionic liquids, unusual thermorheological behavior, and is based on renewable resources. How cool is that?

Ionic liquids are a rather sexy research area these days. These materials are simply salts that are liquid at or near room temperature. Unlike the more common salts made from column 1 and 2 cations and column 7 anions which have very high melting points, both of the ions in ionic liquids are made of numerous atoms, often organic, and are able to spread the electric charge around rather than concentrating it on a single atom. This dispersion results in a weaker ionic bond which can then "melt" at lower temperatures. Most commonly, the vapor pressure of the liquids is quite low.

The researchers used an ionic liquid to dissolve guar gum and make a film that is conductive (no surprise there) but also hardens when heated and softens when cooled. All told, that is quite a package of unique properties to have.

Thursday, June 11, 2009

Mendable polymers

A few months back I was discussing (unhappily) self-repairing polymers, the problems with them and my general dislike of their future. Compare that with this paper on "mendable" polymers. Not a subtle semantic difference, but a totally difference approach - working with (thermally) reversible reactions, either in the polymerization and/or the crosslinking. They are largely relying on the Diels-Alder (DA) reaction, but also other reactions such as disulfide bridges and photodimerization to a lesser extent. When the material needs repair, the reaction is reversed to the monomers, and then re-initiated. Instead of a two-component system in the "self healing" polymers, there's only one component.

The problem here is the limited number of polymer systems that can be easily reversed. You're not going to get too far with plain vanilla polyethylene. Certainly that is a real concern with the monomers, but with the crosslinkers it is a much less concern, as you can have the crosslinking groups as moieties hanging off the backbone. The challenge then becomes a numbers game. There have to be sufficient number of each group so that they can find each other without relying on extensive reptation.

One possible advantage of the DA reaction is that it require two different reactants, the diene and the dienophile. If half of the polyXXX backbone is modified with the diene and the other half of the polyXXX is modified with the the dieneophile, then the reaction within the blend is assured to be intermolecular, not intramolecular. That would not necessarily be assured with the disulfide bridges or photodimerization.

Certainly these are not perfect systems, as they require a separate processing step. The "self-healing" materials do just that - they heal themselves. I doubt that this will be a winner-take-all contest (very little is). I'm just glad there is a second horse in the race.

Wednesday, June 10, 2009

Another Journal Scandal

Yet another tip of the hat to "The Scientist" for reporting this: a completely faked paper of utter gibberish generated by software was accepted by an open access journal (as long as they paid the fees) telling the authors that the article had been peer reviewed. It's pretty clear what the dynamics here are: the publisher was looking to raise revenue, so they took anything the could get. And to speed the process along, they didn't bother with a lengthy review process.

I'be been a big fan of open access for a number of reasons, but this hurts. Not that this couldn't happen in academic journals that are truely peer reveiwed, but the motivation is clearly not there for the publisher, as retractions rflect pooly on them.

What most disturbs me is that publishing scandals of all sorts are occuring with ever greater frequency. That's trouble for other researchers relying on the publications, but also it diminishes the sterling solid perspective that the public has of science.

You may recall that "The Scientist" broke the news on the Merck/Elsevier fake journal catastrophe. They are really on top of this arena. Thank you.

Monday, June 08, 2009

Memory Foam

This is another case of making up a new name that isn't necessary. Also making lemons from lemonade.

"Memory foam" is the hot seller in the matress market, but in my mind, it is merely a compression settable foam. Put a compression on it for a while, and when the foam doesn't bounce back, it's called compression set. This is generally an undesirable property of a material. The Wikipedia article adds nothing to combat this. "it is firmer in cool temperatures and softer when warm." Now that's unusual thermomechanical behavior, isn't it?

Friday, June 05, 2009

GPC- Quantitation that's qualitative

GPC (gel permeation chromatography a.k.a. SEC (size-exclusion chromatography)) is a fairly common technique for measuring the molecular weight distribution of a polymer. A colleague had some results yesterday and in discussing them, it hit me that despite the technique producing quantitative results, I always look at the results qualitatively.

Here's why: the report we were discussing gave several measure of the molecular weight distribution - Mn, Mw and Mz. The first two have a physical;y intuitive meaning, while the last one doesn't. I've seen other reports that even include Mz + 1, also not a physical quantity. The string of all four of these are simple the first through the fourth moments of the distribution.

So the report had a nice set of numbers for all these moments, calculated out to 3 or 4 significant figures and my colleague was trying to make sense of the numbers. That's when it hit me. I only look at the numbers in a "relative" sense (there are two meanings to that phrase - see below). I seldom care about what the exact number of the molecular weight is, only what the changes are between one sample and the next. Yes, the polydispersity index (Mn/Mw) is a helpful as a measure of the distribution's width, but still, I'm only looking for qualitative changes in the distribution, not exact numbers that I can run calculations with. My colleague seemed a little disappointed with this, as certainly we all take strength from numbers, but to me, the numbers do not add anything.

Back to my double entendre on the "relative" results. The paragraph above gave one meaning, but even the quantitative values are relative in that the instrument is calibrated with polystyrene standards and so the results are always relative to this. (Polystyrene can be easily polymerized anionically, so that the molecular weight distribution is tightly controlled.) There are ways to make the measurements absolute (Wyatt's light scattering technique is prominently advertised), but that is still not something I've ever felt the need for.

In this case, we had samples which we were examining for UV degradation and the associated drop in molecular weight. We found this (qualitatively) so we didn't go any further.

And that's unusual for me. One skill that I learned from my advisor during grad school was to get as much information as possible from each experiment and measurement. It's a skill that I now greatly cherish, although I certainly didn't when I was trying to finish up and he kept wanting me to get more info out of my data! It's a skill that my clients always value, but this is one case where just I don't go any further.

Thursday, June 04, 2009

The Queen is Dead. Long Live the Queen

I am greatly saddened with the passing of Koko Taylor, the "Queen of Blues". I thought of her as inseparable from the vibrant Chicago blues scene. Other blues artists roam the world without a hometown, but Koko and Chicago were one and the same. I never did see her perform - I kept hoping that with my son going off to school in Chicago next fall that I could catch her when I went out to visit, but that will never happen. Her last album, "Old School" came out in 2007 and at 78, she still was powerful and aggressive with an in-your-face style. You'd think she would sing forever. She certainly won't be in heaven singing in a choir of angels, but will be over in some small smoky corner doing it her own funky way. God bless.

Tuesday, June 02, 2009

Cap-and-Trade and the Chemical Industry

A new report out looks at the estimated costs of a cap-and-trade program for CO2 emissions, and as you would expect, it doesn't look pretty for the chemical industry. Given that they are up against service industry businesses, this is to be expected.

"For over 80% of the companies in the S&P 500, the majority of greenhouse gas emissions are from indirect sources associated with their business activities. Examples include companies such as clothing retailers which predominantly outsource the production of goods and services, and financial institutions. Many of the S&P 500 companies are service-based and the majority of their emissions result from electricity use in buildings, as well as business travel."

Yet at the same time, "More than half of the greenhouse gases emitted by companies in the S&P 500 are direct from operations", meaning that if you're bad, you're really bad. Depending on which chart you look at, the chemical industry is in the top 3 to 5 worst offenders. Air Products in particular is singled out as the worst offender in the chemical industry (CO2/Revenue) because of the high energy associated with air separation.

This is hardly unexpected. Most chemical of interest have some energy stored into them which is then leveraged later during the reaction, and creating those energetic states requires energy input. Additionally, the increase entropy in ALL purification processes also requires energy input. It's all simple thermodynamics, which the service industry is not constrained with.

Without trying to push a particular political viewpoint or agenda, this report makes it really difficult to see that cap-and-trade would do any other than supply additional support for for exportation of manufacturing elsewhere in the world, while the US becomes more and more of a service industry base. It is doubtful that this would result in the desired CO2 reductions on a worldwide scale, and given the global nature of the atmosphere, the emissions would not drop as expect. The US could feel good however, because "we did our part to cut emissions."

More drugs from Botulism Toxin

You can't get past the first page of any toxicology text without reading Paracelsus's decree: "The dose makes the poison" and that is certainly never more true than with Botox. One of the most toxic poisons, far more deadly than any synthetic toxicant, properly diluted has numerous benefits, with additional uses now being reported.

So how come microbiologists seem immune to the decree? They love to report that there is e.coli/salmonella/campylobacter... in food and that you therefore should trust them when they say don't eat it and thank them when they save your life. Doesn't the concept of an LD50 exist in their profession? Or is it really all about fearmongering?

The Car Industry after GM's Bankruptcy

I've nothing to add to all the commentary about GM. I'm looking at the bigger picture.

As I've mentioned before, this could be real trouble for multiple suppliers to GM, as the court could easily void existing contracts, negate payments and debts and create general havoc on an industry that is already in tremendous stress.

Longer term, I would expect a nice uptick in plastic usage in cars, given the Government's tremendous ownership share of the industry (Do you really believe that no government official is not going to use their influence?? They just can't help themselves, it's what they do, it's their inherent nature) as well as the higher mileage targets. Replacing steels and other metals will plastics/composites will reduce weight, although the real increases are in rolling resistance and drag, not weight.

Monday, June 01, 2009

Supreme Court grants cert for Bilski

The US Supreme Court has granted certiorari for Bilski v. Doll, of great interest to the patent community. The question here is whether or not a claimed invention needs to be tied to a particular machine, article or transformation. At issue here are many of the "business method" patents that popped up after the State Street Bank decision, as well as other more nebulous inventions of intangible items such as computer programs and algorithms, encoded EM waves... The SCOTUS Blog does a nice job of covering the issues, but the legal issues and jargon can be difficult to the uninitiated. Regardless of the outcome (the oral arguments won't occur until next Fall and the decision will be ???), the lawyers will be busy with lots of new fodder to argue about, interpret, reinterpret and so forth until they need another new ruling from on high. (Job security!)

I personally expect that the decision will provide strong clarification on many issues, but will leave other issues untouched. That seems to be the trend with the current court. Oh, oh...let me be trendy and mention that Sonia Sotomayor is clearly for/against this issue because she is__________________which makes her under/over/properly qualified for the SCOTUS.

I'm also still waiting for the resolution of Melendez-Dias v. Massachusetts. It can't be too much longer as the term is nearly over.

And speaking of Supreme Courts, the Minnesota Supreme Court heard arguments this morning over which former New Yorker will be my Junior Senator from Minnesota. I can't say that my state has been hurt in the last 8 months having just one senator; can we continue the experiment a little bit longer? We'd be the envy of the nation as we would have to listen to Senate political TV ads only once every 6 years.