Engineers don’t actually know much about LACs, since almost no LAC has an engineering undergraduate program. So the professor really had no personal experience, unless they had one of the very few Harvey Mudd graduates. I have heard that sentiment a lot from engineering professors, specifically because they have no experience of engineering graduates from LACs, so they are making assumptions, based on what they heard.
It is also very strong in engineering because, not only do they have no experience with LAC students professionally, a very large percent of engineering professors are international, and generally hear of LAC for the first time during grad school or even as faculty. So the likelihood that they will even have known anybody who attended a LAC is extremely small.
I saw a lot of this at the previous two colleges of engineering where my wife worked. In fact, my wife thought the same until she actually met a LAC graduate for the very first time in a professional setting. He was her first graduate student, and he was an absolute star. His career has been amazing, but not academic.
I have not seen that sentiment in Ecology, nor have I seen it in other life sciences with which I have experience.
As for the Biochem prof - that is his opinion. However, the question is whether they would not take a student from a LAC because that student attended a LAC.
All that being said, these are all based on anecdotes or, at best, a limited sample.
The existing data show that percent wise, students who attend LACs are more likely to end up with a PhD. There are many reason that they would want to do a PhD. However, what it also tells us is that LAC graduates are not facing any more obstacles or barriers in being accepted to PhD programs than their peers from other types of institution of higher education.
I mean, even with the common misconceptions of engineering, almost 1/3 of Harvey Mudd graduates end up with PhDs.
Bottom line though (yes, I love writing this), the differences in educational experience (for lack of better terminology) between research universities and LACs is large enough that any effect that attending these colleges has on admissions to PhD programs is washed out compared to how attending affects the success of the student.
Moreover, students can indeed “have it all”. My kid attended an excellent LAC, and also did summer internships at a lab in a top R1. Best of both worlds.