To outside observers, Marijn Dekkers’ departure from the corner office at Thermo Fisher Scientific (NYSE:TMO) might have seemed abrupt. After a seven-year run during which he led a profound re-shaping of the laboratory equipment and supplies manufacturer (and boosted revenues from the $2 billion range to about $10.5 billion a year), Dekkers resigned as CEO of the Waltham, Mass.-based firm to take the helm at German pharma giant Bayer AG.

But from the inside the move likely seemed a lot smoother, as Thermo Fisher tapped long-time COO Marc Casper to take Dekkers’ place. MassDevice caught up with Casper after he’d had a chance to settle into his new role to ask about the move, his views on a potential rebound for large capital spending and his cautiously optimistic take on the economy during 2010.

MassDevice: How did you get your start at TMO?

Marc Casper: I’ve been with the company about eight years. Prior to joining the company I was CEO of a smaller industry participant called Kendro Laboratory Products, and when Kendro was sold to another company in the industry, I joined Thermo Electron at the time, running one of the sectors of the business [Eds. note: SPX Corp. bought Kendro in 2001 for $320 million; in 2005 Thermo Electron acquired the business for $833.5 million] and over the past eight years have taken on other jobs, including chief operating officer of Thermo Fisher a couple years ago, and in September I began the transition process to become CEO.

MassDevice: It seemed that things moved very quickly once your predecessor, Marijn Dekkers, announced his resignation. What was it like to go through such a sea change? What was the biggest adjustment in moving from COO to CEO?

MC: We have an incredible group of employees at Thermo Fisher, incredibly helpful and supportive, so while the job is clearly different all of the colleagues that I’ve worked with here have stepped up and helped me make the transition. We’ve had our senior leadership taking on some of the old responsibilities I had as chief operating officer and Marijn certainly was very helpful to me as I transitioned into the CEO role.

It’s been exciting. It certainly is a humbling experience, but I’m totally energized because the company has such incredible opportunities and such great customers. So there hasn’t been a “whoa moment” in that respect, but certainly Im very appreciative of everyone at the company for all of the commitment they’ve shown to our success.

MassDevice: What’s the biggest leadership lesson you’ve learned, and how and where did you learn it?

MC: The one that I’ve learned and I’ve attributed to a number of the leaders I’ve worked with is always be direct, always be straightforward and candid. We live in a challenging and exciting world. It’s very important for a leader to always give a candid assessment of the world we’re working in and how we’re doing, and to let everyone know the realities that we’re in. I think that allows for a really good environment to continually make a company better and more competitive.

MassDevice: Obviously the economy is in the forefront of everyone’s mind, and the soft capital equipment market has hit a number of companies in our space. What’s your outlook on a potential rebound for capex spending?

MC: When you look at our business, about a third of our business is capital equipment-related and about two-thirds of the business is consumables and services with more of a recurring revenue nature. If you start out with services and consumables piece of the business, the more recurring piece, what you saw in the second and third quarter was clearly activity levels increasing, and certainly in consumables growth returning to near-historic levels. Customers are working again and were you saw a very difficult start to the year, you’re seeing a pretty good level of recurring activity in our business.

The capital equipment piece of the business is one that we hadn’t seen much of a rebound yet, but when we reported our results for the third quarter, we had seen stabilization. First quarter was a continued downward trend, but by the second and third quarter stabilizing but at a much lower level of activity than the prior year.

So we haven’t seen the recovery in that part of the business yet. We’re anticipating that we’ll see a modest recovery, because stimulus dollars are going to be a significant driver of instrumentation sales for us. So that’s a bright spot on the 2010 horizon.

And also the comparables get easier. This year was a difficult year, so next year you’re comparing yourself to a weaker year and that should also help as well. So we’re seeing a stabilization of the economy, easier comparables and stimulus funding that should allow us to return to a growth environment in our capital equipment business in 2010.

MassDevice: Can you talk a bit about the plans for recouping some of the business you’ll lose from the cancellation of the Biosite distribution deal with Inverness? As I understand it, you have a replacement deal in place with another manufacturer. Can you tell us who that is and what the product is?

MC: When you look at our business, we have a healthcare market channel where we’re serving hospitals in North America. It’s about a billion dollar business for us. We’re in most hospitals every day, serving them with their diagnostic needs, lab oratory equipment, consumable, reagents, that sort of thing. Our Fisher Healthcare brand is well-respected in that marketplace. Biosite was a company that we worked with from its inception to build up its presence in North America. It was acquired a couple years ago by Inverness. It had grown to a large relationship and in an orderly fashion that relationship has gotten smaller as Inverness has taken some of that business direct.

As we went into this year and started to look at our plans, we decided it was in our interest to pick a supplier that was going to be growing the relationship with us, as opposed to one that was trimming it back. We found a supplier that we’re excited about. We’re not at liberty at this moment to let that specific company name be known, but next year we certainly will. We’re working with them and we’ll grow that business.

From a total company picture, it’s not a big change in terms of revenue, but any time we’re changing significant suppliers we like to inform the broader world in terms of what were doing.

MassDevice: It’s not the first time you’ve lost a partnership, with Osmetech also choosing to move to a direct sales force. Generally speaking, how does a company plan for and then mitigate the effects of such changes? Are those the kinds of things that keep you up at night?

MC: No, in general we have more people knocking on our door to add relationships than to go away. You’ll see less publicity, we don’t do a lot of publicity when we add a supplier.

Osmetech with a tiny little supplier. To be honest I’m friends with the CEO there [Jon Faiz Kayyem] and he just said that they’re trying to build a small direct sales force and could we help them out.

On the flip side an interesting win for us was the Mass. Biotech Council selecting us as their primary supplier. That serves the community here; all of the biotech organizations typically are members and we’re their primary supplier. That was big win for us in 2009.

MassDevice: So what does keep you up at night?

MC: I would put it in two different buckets. Obviously the economy is one that you have to worry about. It’s not one that you can control, but you have to be prepared to deal with the different scenarios. While we are cautiously optimistic about a recovery, there are obviously scenarios that every CEO has to prepare for. We have to think our way through that and while we remain optimistic on a recovery, you have to prepare for alternatives just in case those happen. I think that keeps you up at night.

And then the other one is obviously it’s a competitive world out there and it’s important that we are the very best we can be every day. Before I go to bed every night I’m just going through the checklist. Are we being the best possible supplier to our customers? Are we meeting their needs? Are we perceived as a great company, helping them solve their challenges? That’s our mission, in terms of enabling our customers to make the world healthier, cleaner and safer. It’s always good to reflect on what we can do better.

MassDevice: What’s on the horizon for Thermo Fisher? Can you tell us about any new products you have in the pipeline, or perhaps new markets you’re looking to enter?

MC: I can give you a few examples, one I’ll pick in analytical instruments, the other I’ll pick in specialty diagnostics. Both are higher-tech portions of our business.

In analytical instruments we’re very well known as an industry leader in mass spectrometry. It’s a business where typically you’re spending between $100,000 to a half-million dollars for an instrument. What we have been very focused on is taking what has historically been a research tool — proteomics research is where a lot of these instruments are used and we have a very special reputation there — we’ve been taking these instruments and putting them into more routine applications.

So that you’re seeing the adoption of mass spec in food safety applications, you’re seeing it in clinical applications, you’re seeing it in environmental applications and you’re seeing a much more widespread use a of mass spectrometers in general and of Thermo Fisher mass spectrometers in particular. That’s been a big focus, it’s a big expenditure for us and we’re excited about it.

The second area is specialty diagnostics. We recently spent about $480 million to acquire a company called B.R.A.H.M.S. AG. B.R.A.H.M.S. is a business that has terrific capabilities in terms of biomarkers in the specialty diagnostics field. We are launching a product for sepsis monitoring in the U.S. It’s the gold standard today in Europe and it’s a product that we think is really important to the healthcare system, because sepsis is obviously a life-threatening infection and having accurate monitoring, especially on how well antibiotics are treating sepsis, is really an important way of improving patients’ outcomes and certainly reducing costs to the healthcare system.

On the flip side, we just launched a new biomarker in Europe called Copeptin, which is a diagnostic marker for heart disease and in Europe is really being used as a companion to the standard of care, which is a Troponin test so that you can get faster results in terms of whether someone’s had a heart attack.

MassDevice: What’s your philosophy as far as acquisitions go?

MC: Our philosophy is to have an active pipeline of discussions going all the time, in good economies, in bad economies, in great economies, because to get deals done they have to first fit three criteria: They strengthen the company’s offering to our customers, they create shareholder value and they have to be “do-able.” You have to have a party that’s interested in doing the deal. It’s easy for us to know which deals will strengthen the company offering. Price is going to determine whether you create value or not, and then the availability is often going to be based on relationships. Do you know the owners? Do you know the CEO? Do you know the executive team? We’re constantly in dialogue with folks to build relationships and identify the right partnerships.

MassDevice: What keeps Thermo Fisher in Massachusetts? Does the state have an unfairly bad rap as being famously expensive and unfriendly to business?

MC: We’re one of the larger companies in Massachusetts and we’re very committed to the community. Not only is our headquarters here, but a number of our divisions are headquartered in the Bay State. It’s been a good environment for us. There’s a good pool of talent here. The access to the research institutions, the access to the great universities here and the great medical centers, makes it an area that is a good place to interact in our field.

The cost of living is high and therefore certain jobs are going to fit more easily here than others, and that’s a challenge, and the tax situation and so forth is a challenge, but we’ve found the benefits of the talent pool here and the access to customers and thought leaders has outweighed some of the challenges that others might have raised.

As a company we worry about education. We want to make sure the next generation and the generations thereafter of scientists are growing up in our community, and we’re trying to put some emphasis on being helpful in that regard.