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From punch cards to high-speed computers: 50 years in the service of research

PORTRAIT: It was actually intended that senior researcher Per Madsen from Center for Quantitative Genetics and Genomics (QGG) should have taken over his parents' farm near Horsens. But his back said no, so instead it was research that called. On 1 September, Per Madsen can celebrate his 50th anniversary in the State's service.

2 pages. That is how much - or little – space, Per Madsen's CV takes up after 50 years. But it is certainly not because he has been lazy. It is perhaps rather an expression of modesty, because if you delve into the individual points, it is half a century of work life that unfolds. And behind the link to his publication list hide almost 300 publications.

I met Per Madsen in his office under the roof in building 1134 on Campus Aarhus, where QGG is now located, to talk about the 50 years that, in his own view, have suddenly passed. And then there is also something about a kidnapping of N. J. Fjord and a police raid that I need to clear up.

From farmer to researcher

You are a farmer by education. What made you go down the path of research?

'- I left primary school after the 7th grade,' says Per. '- I was so tired of going to school, so I wanted to be a farmer, and my parents had a farm a little outside Horsens, which I thought I was going to take over. They had a dairy herd there. But then I got problems with my back, which meant that I couldn't drive a tractor for a while. So, I realized that I was probably not meant to be a farmer, and I decided to go for an agricultural technician degree instead.'

To become an agricultural technician, Per Madsen had to go to an agricultural school. He entered Malling Landbrugsskole, and while he was there, one of his teachers suggested he apply to the Royal Veterinary and Agricultural College (Den Kongelige Veterinær- og Landbohøjskole, colloquially KVL) in Copenhagen. Malling Landbrugsskole had a preparation course for the admission exam at the Agricultural College, which Per attended, and the following summer he sat for the admission exam and passed.

Was it at the level we today call bachelor's that you entered?

'- No, it was a four-year master's degree then. And it went really well. It turned out that I got what we would call a scholarship today, to study a PhD. At that time, it was called a licentiate degree, and I started on 1 September 1974, immediately after I had obtained a master's degree in agriculture,' he says.

So, the reason you went into research was that because you got a taste for it?

'- It was because I got a taste for it, and I thought it was interesting. When I started at Landbohøjskolen, I thought I was going to become a livestock consultant, an adviser to farmers. But then there were many exciting things I got hold of. And in the last year at the Agricultural College, you specialized in what you wanted to work in, and there I became very interested in cattle breeding. And that was my entry into what I have been doing ever since. I did some analyses there, and it was exciting,' Per recalls. '- And that's what I also did in my PhD work, where I worked with cattle data and analyzed it. And then it just evolved from there.'

From punch cards to high-speed computers and High-Performance Computing

You have experienced the whole technological development, from almost no technological aids in the 70s to today, where we have high-speed computers such as QGG's cluster and artificial intelligence. How do you embrace that?

'- Look over there,' says Per, pointing to a shelf behind me. '- That’s a punch card machine. It was used to report data on.'

'- I haven't used that one myself,' says Per. '- But it was used when I finished my PhD. I was employed at what was called The National Institute of Animal Science (Statens Husdyrbrugsforsøg), in the department for experiments with cattle and sheep. The National Institute of Animal Science was then located on the street Rolighedsvej as a neighbour to KVL. This is what later moved to Foulum. When I started at The National Institute of Animal Science, I ran a project to investigate whether it was genetic conditions that caused cows to get mastitis. The project involved 67 herds with extensive data logging, resulting in up to a couple of thousand punch cards per week.  So, I have done data processing from scratch, originally.'

'- And all programming took place on a real punch card machine,' continues Per. '- Not one like that,' he says and points to the shelf, '- that one could only provide numerical data. But all our programming was done in such a way that you wrote the program on paper, then you went to the punch card machine and transferred the code to punch cards, which could then be read into the punch card reader. Sometimes it happened that a punch card got stuck in the punch card reader. Then you had to find out which punch card had stuck and why...'

When did you switch to computer terminals?

'- Yes, we did that in...' Per thinks a bit and then continues: '- We started in 1979, that's when we started having terminals that could be used for something. But still, to begin with, it was over an acoustic modem, where you then called, and it also ran slowly compared to today, but it was a huge advance,' says Per.

'- But then the problem was that it worked over the phones we had in the offices on Rolighedsvej. They ran over a switchboard, and often, when there was an incoming call, the operator would suddenly start shouting on the phone, and it didn't work so well,' laughs Per. '- So we had to explain that when we used those phones, they shouldn't call them, they should find another phone to call.'

But did you program then?

'- We programmed and analyzed data. I had a computer, a Texas, with an acoustic modem on it, so you had to pick up the phone and put it down in two cups, and then it ran at 130 bits per second, and that's insanely slow.'

In the late 70s, they had one (1!) computer at the Agricultural College with 640kb of memory, with some disk stations that were one and a half times the size of a washing machine, and where there could be 30 megabytes on each disk. Back then, disk reading and writing took place with a mechanical arm that moved in and out of the disks. If the disk was put on overtime, Per says laughing, then it would physically start to move.

In 1983, The National Institute of Animal Science was moved to Foulum, but there was no internet connection to anything whatsoever, and certainly not to the NEUCC (Northern European University Computing Centre) at DTU in Lyngby, which they had used for a few years.

'- Just Jensen [today professor at QGG /ed.] and I were the first to move in. We cleaned the offices ourselves of construction dust, and there was actually a period when Just and I drove to the Agricultural Advisory Center in Viby, it’s located in Skejby now, and had office space there for three months,' says Per.

So, it was a relief when it became possible to work in networks?

'- Yes, I was part of the first cluster we had in Foulum. I sat for many years on the computer committee, where we decided to build the cluster. Initially a small cluster, which was located under a laboratory in one of the buildings, but then it was all moved to the old stable office in building 31, I think it was.'

And today we have the QGG cluster, which you also helped to build?

'- Yes, because the cluster we had in Foulum, it was moved here to Campus Aarhus last year, where we are now, and it is Tami [IT administrator at QGG /ed.] who looks after it. I'm not involved in it anymore, but I have been, and it was quite fun to help build something like that.'

DMU

DMU is a package of statistical software developed for applications in quantitative genetics and genomics. The package implements powerful Likelihood based tools to estimate variance components, fixed effects (BLUE), and to predict random effects (BLUP) as well as tools for Bayesian inference about dispersion and location parameter.

The DMU software package

You are one of the initiators behind the DMU software package, which you started in the late eighties?

'- Yes, it was Just Jensen, he has almost the same story as me. He did not study at the Agricultural College, he has an agricultural technician education and was employed as an agricultural technician in our group, where he started analyzing data. Then he was sent to a course in Sweden, where there was a professor from Michigan teaching, and he said that Just should come over and do a PhD. So Just went there and did his PhD and that's where he started doing the first bits of our DMU package, because he had to do some analyses where there was no software that could do the job. So, he was the one who started it, and then I gradually took over the whole thing, and after I went on reduced time, I basically only spend my time at DMU, ​​both on making it a little better, but also to help people use it.'

When you ask Just Jensen about the DMU software, he answers like this:

’- As a colleague, I think it’s fantastic that we have had a person like Per for such a long time, who has been able to continue some of the things we started. And for me personally, Per has been working with DMU for the last many, many years, which was actually something I started during my PhD, but which he then took over and brought forward, and made sure that it became widespread. If it hadn't been for Per, it would never have gained the circulation it has and it wouldn’t have been used so much in the department. I was the one who should have maintained it, but I haven't had the time that he has dedicated to it.'

The milestone

So, it has been one of the big milestones that you moved from Copenhagen to Foulum?

'- It was a gradual relocation because our group, the genetics group within cattle, were some of the first to move over. We moved on 1 April [1983], I think it was...?' Per recalls. '- But that also meant that you moved the family, right? We had just had our eldest son, and we moved from Sjælland before he turned one. We moved over here, and he had his first birthday three weeks later.'

Have you lived in Hammershøj ever since?

'- Yes, we bought a small farm, one of the last state smallholdings to be built. The property was built in 1953 and there are 10 hectares of land with it. There is 2.5 hectares of meadow on the other side of Hammershøj, and then we have the rest around the house. At the time it was built, the barn was equipped with space for 12 breeding cows, a few pigs and a couple of horses. A family could live on that in 1953. You can't do that today,' laughs Per.

Guest lecturer in Zimbabwe

You were a visiting lecturer in Zimbabwe in 1991 and 1992. What did you teach?

'- It was in genetics, primarily in what is called selection index theory. This is what underlies the fact that when you want to create a breeding program, and the breeding goal contains several traits, then you must have determined the overall goal, that is, what is it that we want to breed for, and you do that by using the correlations between traits and the traits’ economic value. The result is a total breeding value, which is a weighting of the individual's genetic potential for all the traits that you want to improve. That was mainly what I was down there to teach,' Per explains.

A significant contribution to the research area

If you were to put into words yourself what has been your greatest contribution to the research field, what has it then been?

Per hesitates a little before answering: '- It has been the implementation of what is called AI-REML [Average Information REML /ed.]. We had a contribution to the 1994 World Congress in Guelph. It is actually the first place that method was presented in a version that can analyze several traits at once. Unfortunately, it took a little while before we got a paper out, and it's a bit of a shame because we should have had that paper finished sooner. We only had a conference contribution. But it has often been referred to, that contribution,' says Per and continues:

'- Also, what we did when we switched to running the test day model for yield on cattle. We were in the process of doing it on Danish cattle in 1996-97, I think it was... But during the course of that project, a collaboration was made, initially between Sweden, Finland and Norway, that we should have a common calculation of breeding values ​​for all countries. Norway then dropped out before it was finished, but the work that went into getting a model made to work across countries, that's also something I contributed to.'

However, long-standing colleagues do not hesitate when describing Per's contribution to the research field over a long working life:

According to honorary assistant professor at QGG, Jan Lassen, who has worked with Per since the beginning of the millennium, Per's contribution to the research has mainly been within the estimation of variance components.

'- In that field he has been one of the pioneers worldwide. Together with colleagues, of course, in making it work. Because it's one thing to have some big, beautiful models of how to create things. And it is even more central today than it was 30 years ago. But to make things work, and then to get them to give some results quickly on some enormously large datasets, which have this genetic structure behind them. There aren't very many people worldwide who can measure up to Per Madsen. There are many and very skilled programmers who have made some program to eat data, as we call it. Then they come to Per, and then Per sit with it for a relatively short time. And he has improved the efficiency of that programming 10-fold or 100-fold sometimes,' says Jan Lassen and continues:

'- He has a completely unique skillset to understand how to easily eat an incredible amount of data and get it through a computer.'

Is it because he can see both sides of the story, both the programming and the understanding of agriculture?

’- Yes, that too... Both the programming part and the scientific part, which lies behind the statistical models. He is also enormously strong there. But he also has the biological understanding of what kind of problems he actually has to solve. He understands that when we collect this data set, it must be collected in this way, because the biological context we want to investigate requires that data be collected in a specific way. Because otherwise we can't do the calculation we want to do. He also has that understanding.'

Just Jensen adds:

'- He was very much the one who was really good at making software, and really good at making it work, and making the computers work. And therefore, it has largely been what he did. And there were a lot of people who needed that, so there were also a lot of people who wanted to collaborate with Per. If you read his resumé, you will also see that he didn't write much himself, but he is the second author everywhere, and he is because he is an extremely helpful person who would like to contribute to other people's projects, so he could focus on creating the methods needed to make it work, and help others do the actual analyses on their own data.'

'- Per has been at the forefront of saying that when there was new technological development, a new way of using the computer, he has been a pioneer in doing so. And the improvements we've seen in the way we can make calculations, that's partly because the computers have gotten better, but it's also largely because the algorithms we've used have gotten better,' concludes Just.

The craftsman

'-If you have a craftsman-like question, you go ask Per!' That was the automatic reaction when one day I asked a colleague in the hallway what he would to highlight about Per.

According to Jan Lassen, Per could just as well have become a craftsman, if he had not become a researcher. When Per and the family moved to the farm in Hammershøj in 1983, Per himself completely renovated the farmhouse and the associated buildings and created a banquet hall with space for 40 people, complete with bar and draft beer system.

'- You can always go to Per, and you don't get advice from Per, you actually get a solution. You can be sure that what Per says, he has complete control over it. And when you go home and do it, if you do it like he said, it works. And he can do that in an incredible number of disciplines. And he is also very helpful at heart. He wants to help, so one thing is that he knows something, but he really likes to share that knowledge,' says Jan.

One of Per's latest projects on the private register is a terrace in the middle of the large lawn by the farmhouse, with tiling, half roof and framed with raised beds. The terrace was dubbed 'grandma's playhouse' when a 4-year-old grandson loudly announced to Per: "Grandpa, it's good that you've built a playhouse for grandma, so she can sit there and finish fuming!"

Per says he doesn't know where the boy got that idea from...

The beer brewer

Per chuckles when I ask him what he does in his spare time.

’- Well, I have my farm that I look after. But then I also brew beer. When I turned 70, I told my wife that when I turned 70, I either wanted to learn to play the violin, or I wanted to brew my own beer. So, she bought me a brewing kit because she didn't want to risk the violin. Or maybe it was because we can't afford to buy me a Stradivarius,' he laughs.

'- As recently as yesterday I had my grain harvested. Then I sent a couple of bottles of beer home with the guy who harvested for me. About an hour after he had driven home, he wrote to me that it was a really good beer!'

Is it a dark beer you make?

’- It was a Belgian dubbel clone. A really good beer. But then, I've made many different kinds. I've brewed 47 so far, and I'd say it's probably three of them that didn't work out, or at least didn't turn out the way we liked. But otherwise, it has gone reasonably well. And I have had great success with the Belgian ones. And the funny thing is that... well, I won't make it before the 50th work anniversary, but I will brew my 50th brew soon.'

How many bottles is that?

'- Well, such a brew, it yields somewhere between 20 and 22 litres. Normally I don't pour my brews into bottles, because it's... When you have something like twenty litres, you have to have 40 half-litre bottles, and you get tired of cleaning them, so I have the beer to stand on kegs instead,' says Per, as he scrolls on his phone to find a picture of the kegs.

It is clear when Per talks about beer brewing that he has found a passion. He is good at it, and the helpers are queuing up, from his three children to colleagues and probably many others.

The good colleague

A standing phrase, when you ask how Per is as a colleague, is that there is always a queue in two places in the department: At the cluster (and before that at the terminals) and at Per's office.

Just Jensen has worked with Per for 48 years, and Per was one of the very first people he had as a colleague, and with whom he talked almost every day for many years about all sorts of small and big problems.

’- I was employed at The National Institute of Animal Science in 1976 and had to start using a computer and all that. I didn't know anything, but Per had his office upstairs, and he was one of those people who was really good at this sort of thing, even back then. And therefore, every time I had problems, I went up and talked to Per. And we have done that many times since then,' says Just, and continues:

’- One of the first things I remember is that Per used the Agricultural College’s small computer centre, and he almost lived over there for several years at first, because he was doing his PhD with large calculations on a central computer system, and everything was read in with punch cards.'

'- I usually say that when you come to ask Per about something, and he is preoccupied with something, he can be a grumpy old man, so there is a small barrier that you have to get over. But when you get past that, he is an incredibly helpful person who really wants to help. It is a very important character trait in him,' Just emphasizes.

Jan Lassen wrote his PhD with Per as main supervisor in the beginning of the 00s, and he is quite blunt in his description of Per as a colleague:

'- I think the general thing about Per is that he saves people's arses. He has done that so many times. After all, he has been the one you have gone to, through the 90s and 00s and 10s. Today, he has a slightly more withdrawn role, but it's absolutely insane the amount of people where he has both saved a student, or a project participant, a main supervisor or a co-supervisor. Because Per just made things work.'

The anecdotes

With half a century of working life behind him, the stories - and the cock-and-bull stories - are lined up. Like when Per, after a world congress in Australia, overslept after a festive evening and didn't catch the plane to New Zealand and the next conference. Or when, as a guest lecturer in Zimbabwe, he was invited to celebrate Midsummer’s eve at Wolle Kirk, a Danish farmer, together with around one and a half hundred other Scandinavians, and folk high school songbooks were passed around. It was also on the way to Zimbabwe in 1992 that Per stopped over in Frankfurt with a colleague from Zimbabwe in the middle of the European Cup final [between Denmark and Germany, which Denmark won 2-0 /ed.], where they watched the second half of the match on a big screen at the airport. Per's colleague made all the Germans around them aware that Per is from Denmark.

But there is still a story that deserves to be unfolded. And that is the story of how a bust of N. J. Fjord was abducted after a party in Foulum.

Who was N. J. Fjord?

Niels Johannes Fjord, colloquially N. J. Fjord, was a docent at the Royal Veterinary and Agricultural College (KVL for short) from its establishment in 1858 until his death in 1891. He founded the Agricultural Research Laboratory at the college, and the experiments in the laboratory and the close collaboration with agriculture and farmers meant that he is considered to be the founder of modern Danish agricultural research. In 1983, Fjord's experimental laboratory, which had changed its name to The National Institute of Animal Science, was moved to Foulum, and that is the reason why, for many years, there was a meeting room in Foulum, which went by the name 'N.J. Fjord's Palace'. The hallway that led down to N.J. Fjord's Palace was called 'N.J. Fjords Boulevard'. After the recent renovation of the buildings in Foulum in 2022-2024 with a view to becoming a campus for three degree programs, the traces of N.J. Fjord have been deleted. Only a white marble bust of Fjord remains on the 1st floor.
Source: Københavns Universitets Bibliotek

The mysterious disappearance of N. J. Fjord

Jan Lassen, who was involved in the kidnapping, explains:

'- The story is that Jette Laursen went from being secretary in the Department of Genetics and Biotechnology, which QGG was then called, to being secretary to the dean, who was then Just Jensen. So, when Just Jensen is promoted from head of department to dean, Jette then becomes Just's secretary. And at that time there was a statue of N. J. Fjord in the department, which stood in Jette's office. She then chooses to bring it to the dean's office, where she is secretary to Just. You don't just do that without anyone noticing. Among others, Per and Morten Kargo and me. So, we abducted N. J. Fjord one day from Jette's office and hid him,' Jan laughs and continues:

'-The statue came home with Per Madsen one evening after a party, and it was fastened with the seat belt on the passenger seat of his car.'

Here it is probably appropriate to get Jette Laursen's version of the matter, so I have been past her office at TECH's dean's office, where she works today:

'- I started in Foulum in 1985, and Per was already working there. And that guy...,' says Jette, pointing to the bust of N. J. Fjord, which stands in a corner of her office, '- he came into the house with one of the last moving loads that came from KVL in Frederiksberg. And the building people, the janitors, as we called them, they were carrying the bust into an archive room. And then I thought, no, he has to come and stand in my office. And he just stood there, and we had a lot of fun with it. At one point we started taking him to PhD parties and graduations and various things,' says Jette and continues:

'Then the sector research became part of Aarhus University in 2007. And the year before, I think it was, Just Jensen was head of research in our department. Our director quit, and Just applied for the position and became director. And I followed him and became his secretary. So, I had to move office and took the bust with me. And all of a sudden one day, when I came to work, N. J. Fjord was gone. He had simply been kidnapped. We made a lot of fuss about it,' Jette laughs at the memory.

'- I got hold of some tape marked ‘crime scene’ and had it cordoned off, and I searched high and low. And then all of a sudden, I got an email from N. J. Fjord. A hotmail account had been created in his name. So, we corresponded back and forth. And on a regular basis, pictures came in of N. J. Fjord being on a hot air balloon ride over Paris and windsurfing in Hawaii and everything. And there were also some pictures where Per had taken him to, I think it was a PhD party, and he had him sitting in the front seat of the car with a Santa hat on.'

As Jan Lassen remembers, Per got caught in a police raid that evening. Per – who had not drunk anything – sat in his car with the bust of N. J. Fjord next to him. And had to talk himself out of that.

Per, how did you talk your way out of that situation?

'- I wasn't stopped,' says Per. ’- It was a celebration of 2 PhDs at the end of November, and we had brought N.J. Fjord to the party. I had to take him home, so wearing a Santa hat, he was placed in the passenger seat of my car. When I passed Ørum on my way home, I saw a couple of officers standing next to a car talking to the driver. In order not to catch their attention, I quickly took the Santa hat off N. J. Fjord. I was not stopped.'

Subsequently, Jette called the kidnappers to a meeting:

'- And then appeared Jan Lassen, Per Madsen, and Morten Kargo, in black suits, black shoes and sunglasses. I had had a table made that I had an IT employee help with. We had tons of screens set up and there were wires and cameras everywhere. And then we had made a sign that said, 'hidden camera'. It wasn't hidden, but that was the fun of it. And then we had the meeting and drew up a contract, which exists to this day. It stated that N.J. Fjord was to stay with them in Foulum from 1 October until the Christmas party. They made a pedestal for him to stand on. At that time, they had just rebuilt K21, where the bust was to stand, and at the end of the hallway there was a large meeting room. It was simply named N. J. Fjord’s Palace, and the hallway to the meeting room was named N. J. Fjord’s Boulevard.'

'- Then there was a bit of trouble with the compliance with the contract, but it doesn't really matter, because the funny story is exactly that with the contract and the whole setup and all the fun that was made out of it,' says Jette.

And today he is standing here in your office in Aarhus?

'- Yes, now he's standing here. He has been here for a long time. And he got the tie as a goodbye present from Brian Bech Nielsen. Before becoming rector, he was dean of the large Science and Technology faculty. Brian thought N. J. Fjord should wear a tie, so he got him that silk tie. And for Christmas he wears a Santa hat, Santa beard and glasses,' Jette concludes, laughing.

Jan also remembers the whole thing as a really good round of fun and games: '- Then we negotiated the agreement, and it was signed. It has petered out a bit since then, but Per has laughed about it a thousand times. He thought it was so funny. It's just Per.'

On the domestic front, Per has another 50-year anniversary coming up, but that is a completely different story...