Bad actor PI + young grad students = non va bene

I really haven't covered the Ranga Dias superconductivity story, but Nature's news section has really got the goods on it (article by Dan Garisto): 

...But the measurements were plagued by systematic errors, which students say they shared with Dias. “I was very, very concerned that one of the probes touching the sample was broken,” one student says. “We could be measuring something that looks like a superconducting drop, but be fooling ourselves.” Although students did see resistance drops in a few other samples, there was no consistency across samples, or even for repeated measurements of a single sample, they told Nature’s news team.

Students were also worried about the accuracy of other measurements. During elemental analysis of a sample, they detected trace amounts of nitrogen. Dias concluded that the samples included the element — and the resulting paper refers to nitrogen-doped lutetium hydride. But further analysis, performed after the paper was submitted, indicated that nitrogen was not incorporated into the LuH. “Ranga ignored what I was saying,” one student says.

Because they were not consulted on the CSH paper, the students say they wanted to make sure they were included in the process of writing the LuH paper. According to the students, Dias initially agreed to involve them. “Then, one day, he sends us an e-mail and says, ‘Here’s the paper. I’m gonna submit it,’” one student says.

E-mails seen by Nature’s news team corroborate the timeline. Dias sent out the first draft of the LuH paper in an e-mail at 2.09 a.m. on 25 April 2022. “Please send me your comments by 10.30 AM,” Dias wrote. “I am submitting it today.” The manuscript they received did not contain any figures, making it difficult to assess. The students convinced Dias to hold off on submitting until the next day, when they could discuss it in person.

One student was upset enough by the meeting that they wrote a memorandum of the events four days afterwards. The memo gives details of how students raised concerns and Dias dismissed them. Students worried that the draft was misleading, because it included a description of how to synthesize LuH; in reality, all the measurements were taken on commercially bought samples of LuH. “Ranga responded by pointing out that it was never explicitly mentioned that we synthesized the sample so technically he was not lying,” the student wrote.

The students say they also raised concerns about the pressure data reported in the draft. “None of those pressure points correspond to anything that we actually measured,” one student says. According to the memo, Dias dismissed their concerns by saying: “Pressure is a joke.”

Students say that Dias gave them an ultimatum: remove their names, or let him send the draft. Despite their worries, the students say they had no choice but to acquiesce. “I just remember being very intimidated,” one student says. The student says they regret not speaking up more to Dias. “But it’s scary at the time. What if I do and he makes the rest of my life miserable?”

Dias made some changes that the students requested, but ignored others; the submitted manuscript contained a description of a synthesis procedure that had not been used. He sent the LuH manuscript to Nature that evening.

This is an unusually thorough article about a situation where it is pretty clear the PI is a bad actor, intent on lying to the scientific community.* I cannot imagine graduate students (all probably younger than 25) being forced into this situation, especially since they don't know that a PI making claims on a paper that cannot be backed up by data is WEIRD and a solid sign that they should leave their adviser immediately. 

Derek Lowe wisely pointed out the difficulty in leaving a graduate adviser. He likened it to leaving a wedding at the altar. I am not quite sure that is quite the right analogy, but I gotta say, it's in the ballpark (i.e. joining a graduate research group is more like joining a small family than it is like joining a workplace, leaving a graduate adviser is more like openly leaving a team because of a coach more than it is like quitting your job at McDonald's because of a bad shift supervisor.) 

It makes me wonder if incoming graduate students need a small booklet that tells students that they have rights, and that going to the department chair because a new assistant professor is intimidating them over data integrity concerns is an okay thing to do. Until that day, this real but rare thing will just keep happening. 

*what is weirder is that if you're going to publish this in Nature, gee, it's going to attract some attention. So what's the ROI on lying? 

Housing is really expensive for graduate students

In this week's Chemical and Engineering News, an important conversation on chemistry graduate student finances (article by Wynne Parry): 

Housing, in particular, can strangle students’ finances. The high cost of living near the University of California, Santa Cruz, drove graduate students at this institution to strike in December 2019. They demanded a $1,412 per month raise, an increase they calculated would allow students to spend less than 30% of their pretax income on rent, the proportion recommended by financial experts.

On July 1 of this year, Connor Brandenburg, an organic chemistry student at UC San Diego, got a raise that brought his finances nearly in line with this rule. After his department increased students’ stipends from $31,000 to $34,000 per year, his rent—$897 a month for a studio in university-run housing—accounted for about 32% of his pretax income.

But, within a year and a half, this share may grow substantially. In April 2023, he will have exhausted the 2 years of on-campus housing the university allotted him as a graduate student. Off-campus rents for a comparable studio can run up to $1,700, Brandenburg says, so he’s planning to downgrade.

“I’m 24. I don’t necessarily want to share a room with someone anymore, [but] financially, that may be my only option,” he says.

There are aspects of short-term pain/long-term gain for graduate school, but it seems more than a bit cruel for this to extend to penury in the form of immediate housing costs. Establishing some kind of reasonable ratio for student stipends to rent should be a goal for departments - of course, that's easier said than done. 

How many 1st year grad students will get their Ph.D. in chemistry?

A little evening tidbit: Dan Drezner is a professor of international political economy and a longtime foreign policy blogger. He's been involved in an interesting debate about whether or not a Ph.D. is required for going into policy in the Washington, D.C. area. He is pushing back strongly against any encouragement of a doctorate as a terminal degree. Here is a tibdit from his latest long post about it that I found stunning:

Furthermore, not finishing a Ph.D. is not exactly uncommon.  Click on this slide show about Ph.D. attrition rates from the Council of Graduate Schools, and note the following three facts: 

1)  Only 46% of all entrants finish their Ph.D. after seven years in a program.
2)  For social science Ph.D.s, that figure is even lower -- 41%
3)  If you extend it out to ten years, the lowest completion rate among the social sciences is political science -- only 44% complete a doctorate after a decade.  In other words, entering a Ph.D. program and then not finishing is the modal outcome. 

From that report (written in 2008, collected from data before then) the 10-year completion rate was 62% for a doctoral degree in chemistry. (I wonder what that number is now? To SESTAT!)

When are opportunity cost arguments most applicable?

Yesterday, a great many chemistry bloggers answered Mr. David Bernstein's question (posed on the Washington Post's education blog) "Why are you forcing my son to take chemistry?" I cannot really add anything to their righteous responses, so I'll send you over to Ash's, Derek's, SAO's and Janet's.

[Won't someone speak up for the joys of memorization? Very first, I assume that Mr. Bernstein is deeply mistaken about general chemistry being all memorization. Second, does anyone actually teach chemistry by memorization? Third, I've always felt that remembering something was the byproduct of actual understanding of the concept. People don't like memorizing things that are "useless" -- like the ordered list of American presidents, their parties, dates of office that I was asked to memorize as a student of AP US History (a special demand of our excellent teacher -- hello, Dr. P!) But it's only a memorized list if... you don't understand the ebb and flow of American politics. Do you memorize the alphabet, or do you understand it? Hard to say. Did I memorize Jeff Saturday's jersey number? (63, btw) Not really.]

I felt the biggest pang of potential regret when I read Mr. Bernstein's final argument:

There’s a concept in economics called “opportunity costs,” which you may not have learned about because you were taking chemistry instead of economics. Opportunity costs are the sacrifices we make when we choose one alternative over another. A family store may be turning a good profit by selling tomatoes, but it would turn a bigger profit if it used the same shelf space to sell cucumbers. There are opportunity costs of selling tomatoes. 

When you force my son to take chemistry (and several other subjects, this is not only about chemistry), you are not allowing him that same time to take a public speaking course, which he could be really good at, or music, or political science, or creative writing, or HTML coding for websites. 

Maybe he will learn something in chemistry somewhere along the way. But he will lose out on so many other more important opportunities, and so will our society, which will have deprived itself of his full contribution.

As someone who routinely uses "opportunity cost" arguments against the "STEM graduate school is good for you" meme, I am concerned that perhaps Mr. Bernstein's argument sounds a little too familiar.

But the opportunity costs of one year of high school chemistry seem relatively low. While Mr. Bernstein seems to have stipulated that it's not just about chemistry, I don't understand how it is chemistry that HAS to be the marginal class that has disallowed his son to not take a course in creative writing or HTML coding. At the same time, the relative opportunity costs of taking a Ph.D. in the sciences seem potentially very high. While we can debate the amount of time Mr. Bernstein's son might spend taking chemistry, we can all agree that a rigorous science graduate program will consume all of one's attention for at least 4 to 5 years. That you could be doing something else during that time seems apparent.

I also think there is also a distinct difference between the life of a high school student (15-18 years old) and a potential graduate student (somewhere between 22 and 28). When you're a high school student, it seems like there are very few options that you should look at and deny yourself. (Perhaps professional athlete or professional entertainer?) When you're in your late 20s, I think you should be thinking very seriously about how you will be making a living, and what your chances of success might be. Denying yourself options in high school seems a little unwise; by going to graduate school in the sciences and pursuing a doctoral degree (and beyond!), I feel that by pursuing one path (academic/industrial science), you are continually choosing not to walk other paths or raise the cost of pursuing them later.

Well, whaddya know? "A cost to the individual and society"

From an astute reader, a conversation with the authors of "Is American Science in Decline?" (by sociologists Xu Xie of the University of Michigan and Alexandra A. Killewald of Harvard). This interview was published by Salon.com:

Let me start with the obvious question: Is American science in decline? 

No I don’t think so. I think the evidence that we put together is pretty convincing that, by most measures, American science continues to be very strong and in some spheres even  improving. We do find some areas of  concerns in terms of the wages of scientists. And when we turn to the international perspective, that’s a little bit of a different story. Other countries are gaining on the U.S. but compared to the position that science has held in the past in this country, it’s still quite strong from a historical perspective... 

[snip] Some analysts see the problem differently. They talk about a surfeit of scientists? 

The growth of post-doctoral appointments has been a concern for many people, that these appointments are becoming a kind of holding tank where you’re delaying your first real job longer and longer and folks who aim to become academics are unable to find permanent employment. On the other hand, it’s not clear that it’s bad to have people with PhDs in non-academic positions So I think it certainly can be a concern as relates to an individual’s choices. If someone makes an investment that retrospectively they wouldn’t have made, that certainly is a cost to the individual and society. But I think the fact that individuals who get PhDs end up in other places is not by itself a bad thing. (emphasis mine)

I will continue to argue (perhaps too stridently and perhaps ignoring other data) that ignoring of opportunity cost is something that young scientists-in-training do at their peril, especially in a relatively low job growth economy.

What online graduate degrees in chemistry are missing: group meeting

About a year ago, I wrote up a little criticism of the University of Florida's "Master's Program in Pharmaceutical Chemistry". I mainly focused on the tradeoff of cost; that is, in a typical master's program in chemistry in the United States, they pay you*. In a distance program, you pay them; $16,800 for the UF program, it looks like: 32 credit hours X $525/hr. I also cast doubt on the willingness of employers to accept this credential over a traditional M.S. degree. 

 A few weeks ago, a comment showed up on the post that I publish in part here:

I'm part of this program and the material is no "cake walk", and they use several tools to adequately "compensate" for anything potentially lacking due to the inherent nature of distance learning (with a possible exception for benchwork which most students already have in spades given that most of them are currently working in the industry---and which others already have from undergraduate or additional studies).  

As to certain employers not viewing this degree as having the prestige of a "live" program---screw 'em. Any employer in today's world that automatically, totally discounts an on-line degree is an inflexible dinosaur (with a higher likelihood of failing) that I likely wouldn't care to make a career with anyway. While they are certainly free to question the sufficiency of a particular individual's preparedness (as they would any job candidate), and while the school has certainly adapted to find new ways to raise some revenue in this more interconnected world; this particular degree is sound, and anyone completing it should be viewed as being self-disciplined enough to complete a major project without much prodding/nursing.  

I do not believe the school is overselling the usefulness of this degree. No one has promised me I'll be able to secure a golden ticket at the end of my studies. However, they likely do not want to advertise in big letters that the U.S. medicinal chemistry market is likely oversaturated in the short term with very skilled people. 

I don't know if I agree with this statement; I found it somewhat unconvincing. But, as I thought about it, it brought to my mind one of the benefits of bricks-and-mortar graduate school: group meeting.

I don't really miss group meeting very much. I spent a lot of time being very bored by it. But to be sitting in a room for (at least!) 2 hours a week, 45+ times a year with my professor and his students, discussing our research results, research results in the literature and (occasionally) the direction of the industry was really, really important and formative. You learn how to analyze other people's results, how to think critically about the literature and to sit and listen to your professor's opinions and the opinions (informed or not) of your colleagues. I think I learned all the important principles of organic reaction mechanisms (again and again and again) by sitting in a windowless room lit by fluorescent lights with uncomfortable chairs, trying to figure out why you get this isomer as opposed to that isomer. Where are you going to learn how to answer questions under fire? Where are you going to learn how to defend your research results? I do not believe that distance learning can simulate this experience.

As I said, at some point in the future, I'm sure that distance-based graduate school will be equivalent to a traditional program and these technological hurdles will somehow be overcome. But for the moment, I do not think that you will learn as much in a distance program as opposed to a traditional master's program.

*Granted, there is opportunity cost to be calculated. 2 years in school is 2 years out of the job market. 

What Jon Bardin misses: the costs of graduate school

A recent commentary in The Chronicle of Higher Education by neuroscience graduate student Jon Bardin restates a lot of the truths about graduate school: that tenure-track positions in the biomedical sciences are extraordinarily hard to come by, that graduate school is a great place to learn effective communication skills and problem solving and that graduate school mentors need to learn to guide their students towards paths away from academia and towards 'the real world.'* However, what marks Mr. Bardin's essay is an air of nonchalance towards the typical "What did I just do?!?" panic of typical senior graduate students. He tends to lean heavily on the 'alternative career' path, as you can see from the following excerpts:

...These are experiences and skills that will carry me through many dark days as a writer. But the same skills would have benefited me if I were leaving for the pharmaceutical industry, or for consulting, or to open a microbrewery. Everyone needs a problem solver, an articulate communicator, a thoughtful arbitrator. If graduate students can learn to approach their education as a series of learning opportunities rather than a five-year-long job interview, I think many who choose to leave would find that they had not wasted their time but rather that they had learned a great deal in a safe environment, while being paid, to boot. (emphasis CJ's)

...A few months ago, I attended an event sponsored by several local biomedical universities titled "What Can You Be With a Ph.D.?" The event was spread over numerous auditoriums and included panels on science writing; teaching at the elementary, high-school, and college levels; government jobs, both in bureaucracy and research; forensic lab work; nonprofits; finance; biotechnology; consulting; and, yes, even postdoctoral research. Roaming from panel to panel, I was amazed at the sheer scope of opportunity for science Ph.D.'s. The event reinforced that, as the world becomes ever more data driven, our experiences in collecting and analyzing data make us increasingly valuable commodities in any number of fields. Looking around, it became clear that we've been looking at this pyramid upside down.

Here's what I think Mr. Bardin's essay elides: cost. His Ph.D. education (and mine) were paid for by the US taxpayer. Is this the best deal that the taxpayer can get? As I've said in the past, I think society gets a pretty good deal: they get 5+ years of cheap labor in science, (hopefully) contributions to greater knowledge and, at the end of the process, they get a trained scientist. Usually, that trained scientist can go on to generate new innovations in their independent career in industry or academia. It's long been my supposition that the latter will pay (directly and indirectly) for the former. If that's not the case, is this a bargain that society should continue to support? 

Mr. Bardin also shows a great deal of insouciance about the costs to himself: what else could he have done, if he hadn't gone to graduate school? When we talk about the costs of getting a Ph.D., I believe that we don't talk enough about the sheer length of time (5+ years) and what other training might have been taken during that time. Opportunity costs matter! An apprenticeship at a microbrewery (likely at a similar (if not higher) pay scale as a graduate student) or a 1 or 2 year teaching certification process easily fits in the half-decade that most of us seem to spend in graduate school. Are the communications skills and the problem-solving skills that he gained worth the time and the (opportunity) cost? Could he have obtained those skills somewhere else for a lower cost? 

This last problem leads me to a core dilemma of alternative careers for Ph.D. educated scientists. In the range of careers that Mr. Bardin uses to suggest "the sheer scope of opportunity for science Ph.D.'s", in how many of these fields will a science Ph.D. be an entry-level credential or an advantage? Patent law, for example, offers (or did?) Ph.D. chemists an opportunity to increase their wages significantly versus a career at the bench. How many of these fields would see a science Ph.D. as a wild overqualification (i.e. elementary education?) Would someone in one of these careers welcome a Ph.D. scientist or see them as a usurper of positions away from whatever entry-level credential that's preferred? This is a problem to be confronted, not wished away. 

While I sincerely hope that "as the world becomes ever more data driven, our experiences in collecting and analyzing data make us increasingly valuable commodities in any number of fields", betting over 50% of your 20s on that hope seems like a risky proposition. 

*BTW, I'm getting bored and irritated with these sorts of comments:

Crucially, they [professors] must make it clear that leaving academe does not suddenly brand them a waste of their mentor's time... But too many young scientists are made to feel worthless because of their desire to leave academic science. It has to stop.

Perhaps it's the fact that most chemistry graduate students (used to?) end up in industry. But your self-worth shouldn't be dependent on whether or not you can become a tenure-track professor and the vagaries of your mentor's evaluation, true or not.

UMich student let go because of associations with grad student unions?

I don't know if this has been covered elsewhere in the science/chemblogosphere, but I thought it was interesting. It's the story of a dispute between materials engineering graduate student Jennifer Dibbern and her faculty adviser, Rachel Goldman, over efforts to get the research assistants in the department to join the graduate student instructors union:

Former engineering GSRA Jennifer Dibbern claims that shortly after informing her faculty adviser she was an advocate of forming a student researcher union she began receiving poor reviews and was ultimately dismissed. Dibbern said she was essentially told by her adviser to cease her involvement in unionization efforts. 

[UM provost] Hanlon, however, says that's not the case and that Dibbern's account of her dismissal, which she shared during a news conference Wednesday, is incomplete.
"I have personally reviewed the academic record for this case and I'm convinced that the academic decisions made by our faculty were justified and appropriate," Hanlon said, adding that faculty "followed a thorough and fair process and I want to offer my strong support for them."

Here's some of the timeline, as provided by the graduate student union:

August 5: In an individual meeting (called to discuss data) Goldman stated that she wanted to go to the MERC hearing Monday as she feared the union would ruin grad education at U of M. She relayed conversations she had with graduate students who were involved in the No Campaign. In the conversation, she referenced the consent agreement reached between GEO and the University regarding terms of election and said she was following the situation “very closely.”  She then stated Ms. Dibbern had more data than they could review in that meeting and that they would discuss it the following week. 

August 8: At a 10am individual meeting, Goldman reviewed the GEO website and spoke about it with Ms. Dibbern.  She stated that the MERC meeting will determine whether "we have a research university left." She stated she would leave if the union was formed. 

August 8: Goldman sent Ms. Dibbern an email that, for the first time, questioned the progress she was making on research and instructed her to stop all outside activity to demonstrate her commitment to her research. 

August 10: Goldman repeatedly instructed Ms. Dibbern to stop all outside activity, this time in
person.  When Ms. Dibbern asked for clarification, Goldman stated, "you know what I mean."

Here's a snippet of a blog comment from one of the union's stewards, Dan Hirschman (who is speaking for himself.) Go over and read it -- it's much longer and very informative:

Although Prof. Goldman has a reputation for running a very intense lab, no other student was ever told (to my knowledge) to curtail other outside activities (such as participation in sports, or family obligations). The first allegations made by Prof. Goldman of specific failures were in the email linked above, dated August 8 (after having favorably reviewed Dibbern’s progress just two months earlier). Prof. Goldman fired Dibbern just three weeks later. 

So Dibbern and the union seem to have a couple grievances:

• Professor Goldman seems to have fired Ms. Dibbern not because of any poor performance, but because of her enthusiasm for unionization. 
• Professor Goldman did not follow established procedures for removing a research assistant.

I think this story is interesting because it lays out the current balance of power between professors and graduate students at top research departments in the US. If the professor doesn't like the graduate student for any reason, they can be removed (counter to the university's own policy!) and the administration will make it very clear that they're going to back the professor, not the student. Graduate students (and especially undergraduates considering graduate school), be aware of this possibility.

If it is indeed true that Professor Goldman runs an intense laboratory, one of her funded students should be aware that announcing that you'd like to get involved in a political and organization effort outside of your laboratory research is really unwise. It may not be fair, but is it worth 2+ years of your research career to die on that hill? (...And this is how the balance of power will continue...) 

I'm also discomfited by the suggested solution by Mr. Hirschman (the union steward):

One brought up above is the ability of PIs to fire research assistants for whatever reason they chose, and how often that is used. At least at Michigan, it is not uncommon for a student to switch labs or to leave a program with just a master’s degree because of disagreements with a PI - personal or professional. That is precisely one of the most important reasons why GEO has pushed to bring RAs into the union (currently graduate student instructors (aka TAs) are covered, but not RAs). PIs should have the ability to fire students who fail in their research tasks, but they should be required to prove that the student has actually failed. (Whether or not PIs should be able to demand 80-hour work weeks and forbid their RAs from taking Christmas vacations is also something that will hopefully be up for negotiation – bearing in mind the complexity that many RAs work on their own projects in conjunction with their paid work.)

"Prove that the student has actually failed"? That sounds like a high bar (depending on who's doing the measuring, of course.)

A chemistry grad student talks about money worries

Not much time to blog today, but I enjoyed the recent interview by NPR's Planet Money of one Diogenes Placencia (what a wonderful name!). He's a chemistry doctoral student who grew up poor in the Bronx and is now ABD at the University of Arizona:

Do you worry about money?

Constantly. I worry mostly about my mother. I worry about providing for her when she gets older, and giving her some good years.

Are there any recent purchases you regret?

I really don't regret anything, because I put everything through such a rigorous process of whether I should get it or not. I do a cost-benefit analysis.

So what was the last purchase you put through this process?

It was an arm-band for my iPod. I swear it was like $15, and I looked at it for two months.

What's the next thing you're going to buy?

A pair of flip-flops.

Have you gone shopping for flip-flops?

I went around the other day and I looked at some. And I was like, "Oh, 20 bucks. That's a lot."                            

A son like that will put a smile on a mother's face.

Money tips for grad students

I have a few more points about graduate school and personal finance. (Why isn't this sort of thing covered by graduate schools? I mean, you'd think it wouldn't be that hard for someone to come up with a glossy one-pager that would help out the students that are going to be populating your halls for the next 5 years...)

The taxman interfereth: An astute commenter (Anon709p) notes that, if you're being paid by a graduate student stipend (rather than a salary), you are not allowed to contribute to an IRA. (IRAs are meant for people who have taxable income.) The law around this is a little complex, but a good indication is that if you're not paying FICA taxes, you can't use those funds to fund an IRA. Doesn't mean that you can't save that money up, which brings me to my next point...

An emergency fund: Starting out in graduate school? First time that you're making your own money? You should probably save up an emergency fund of some sort. A good rule of thumb is that it should be about 2 to 3 months' worth of expenses (rent, groceries, gas, car insurance, etc.) Remember, it's an emergency fund, not a fund for quick vacations to Panama City.

Credit cards = mostly bad news: If there's anything to be learned from the last 3 years, it's that credit cards and other forms of consumer credit can be really, really harmful to your medium-term and long-term plans. I'm not saying that you should cut up your awesome American flag Discover card, I'm just saying that running a balance will cost you. But you knew that already, right?

Student loans -- what are they good for?: Should you get a student loan? That's a really tough question, balancing your long-term employability and financial goals against short-term quality of life.

If it's genuinely going to increase your quality of life (e.g. you really like your sleep, so you don't want a roommate), it might be worth it. But if you're taking a student loan so you can afford short-term consumption (dinners out, spring break in the Outer Banks, microbrew sixers instead of Natty Ice), this is a bad idea. If you get a postdoc, you will be on the hook to pay that loan back six months after you graduate -- and you know how lucrative those postdocs are. Don't forget, student loans obligation are darn near impossible to escape, even in bankruptcy. Treat them like thionyl chloride -- useful, but dangerous.

Why grad students should think about contributing to an IRA

It's not easy being a graduate student -- chances are, you're not making a lot of money and you're definitely not thinking too much about retirement. Nevertheless, retirement is coming your way, and it's not a terrible idea to start thinking about how you're going to prepare for it. Hopefully, this post will go a little way towards starting a long-term conversation about the 5+ years that people trade for a degree. One of the clearest places where there is a tradeoff is in retirement savings (typically done in the US with 401k plans and IRAs.)

Assume that we have 3 individuals. They all graduate from college the same year, they're all the same age, gender, whatever. At year 0, they decide to take 3 different paths, as shown below:

Chemist A: takes B.S. immediately, goes to work for 50k, gets 1% raise a year, contributes 5% of salary to a 401k, gets a 1.5% match. Chemist A contributes 3k every year to an IRA. All investments get 5% return.
Chemist B: goes to grad school, gets Ph.D. in 5 years, goes to work for 80k, gets 1% raise a year, contributes 5% of salary to a 401k, gets a 1.5% match. After graduating, Chemist B contributes 3k every year to an IRA. All investments get 5% return.
Chemist C: goes to grad school, gets Ph.D. in 5 years, goes to work for 80k, gets 1% raise a year, contributes 5% of salary to a 401k, gets a 1.5% match. In Year 1, Chemist C contributes 3k to an IRA (life savings?) and only $500 a year for the rest of graduate school. All investments get 5% return.

After 25 years, what are their total nest eggs?

Chemist A, B.S. (year 25 total nest egg): $314,125.04
Chemist B, Ph.D. (year 25 total nest egg): $285,501.86
Chemist C, Ph.D. (year 25 total nest egg): $300,895.18

The spreadsheet is here, if you would like to check my figures.

From this point of view, the 5 years in graduate school will "cost" somewhere around 30k in retirement savings (all things being equal.) With a $5,000 investment during graduate school, you can recover about 15k (or about 50%) of those lost retirement savings.

Now, the caveats to this sort of figuring are pretty darn long, but let's list a few. First, it's a little bit unfair to compare a 25 year career with 20 year careers. Also, Chemists B and C could put more of their salaries into their IRAs (you'll note their 401ks end up bigger than Chemist A.) Do remember, their net worths could be very different, too. There aren't big promotions figured into this calculation, or job switches, or layoffs or any of the other things that actually make up real life. Chemist C could have a nasty gambling habit, Chemist A could enjoy investing in real estate in Belize, no investment this side of Bernie Madoff has a steady 5% return with no dips, you get the idea.

Going to graduate school for an extended period (longer than 2 years?) basically puts parts of your life on hold. Whether or not you want to admit it, there are costs associated with that pause; contributing to a very basic IRA (Vanguard Total Stock Market Index, anyone?) might be a way of alleviating some of those costs.