Chip Kelly: “I’ve had a lot of respect for Jimmy and Greg Roman going against them. They can scheme up the run game as good anybody I’ve ever seen.”

This is the transcript of Chip Kelly’s Wednesday morning conference call with Bay Area reporters.

Q: Is there anything you can put your finger on for why you’ve had to come back from big deficits the first three games?

KELLY: Part of it is the opponent. You’ve got to give credit to them for playing well. I think every week in this league is a battle. There aren’t many blowouts in this league. I think every game is close. Every game comes down to the fourth quarter. I think sometimes that gets lost in it – you need to give credit to the other team.

Q: Are you finding that your team is better equipped for the third and fourth quarter than the opposing teams?

KELLY: We’ve always felt our team is in good condition to play a full 60 minutes if that’s the question.

Q: It is the question. Are the training methods something you took from New Hampshire or Oregon? When did they come about as far as your coaching philosophy?

KELLY: We’ve always wanted to be, no matter where I’ve been, a well-conditioned team. We never wanted to lose a game because the other team was in better shape than you. You wanted to leave it up to which team executes the best and which team plays the best, not which team is in the best shape. Everywhere I’ve been, our teams have always been very well conditioned.

Q: From watching the tape of Sunday’s game, what stood out about the 49ers in their loss to the Cardinals?

KELLY: I think they’re obviously an outstanding football team. They got hurt with penalties, especially on third down there in the second half, allowed Arizona to convert some plays on them. They obviously were a little bit different on offense than they had been when they came out in five wides and four wides and a lot of different looks that they normally don’t do. I think that may have had something to do with Vernon Davis being out. But one thing you know about them offensively is they’re going to give you some exotic looks that you’ve got to be prepared for because they do such a good job with it. I think some of the five-wide stuff, which was new to them, and then really I thought the defense played well but I thought the penalties hurt them.

Q: Aside from the five wides, when you watch the 49ers on film do you see a lot of teams from Stanford in there?

KELLY: No, I think they’re different a little bit. They’re a little bit more exotic than they were even at Stanford I think, maybe because they have more time with their players and they’ve got smart players on the offensive side of the ball. I’ve had a lot of respect for Jimmy and Greg Roman going against them. They can scheme up the run game as good anybody I’ve ever seen.

Q: How surprising were the five wides to you as someone who’s gone against them a couple of times?

KELLY: I don’t think anything is surprising when you’re play against a Jim Harbaugh or a Greg Roman team. I think they’re going to use every weapon available to them. They’re always working to gain an advantage so I wasn’t surprised when they did it. It was just one of those things, you chuckle to yourself, “They’ve got another wrinkle now.” They’re always going to have a wrinkle and they always find a way to be successful on the offensive side of the ball.

Q: What about the defense? What do you remember from facing Vic Fangio and does that unit bear and similarities to his unit at Stanford?

KELLY: He’s been a 3-4 spacing guy. Does a lot of different things in a Nickel package, so he’s similar from that standpoint. But the one thing that just stands out with him defensively is just the players. Patrick Willis is arguably one of the best inside linebackers in the league. Justin Smith is everything you want in a 3-4 defensive end. (Ahmad) Brooks can rush the quarterback on the outside. Ian Williams is playing at a high level. That front seven is very formidable and it sticks out to you.

Q: With your offensive line sustaining some key injuries, do you have confidence that the backups stepping in can hold up and you still can have an effective line?

KELLY: Yeah, we feel confident in our guys. We felt our second offensive line did a very good job in the preseason when they had an opportunity to get in there. We think, by the style that we train, our guys get a lot of reps in our training sessions. Gives them an opportunity when their chance comes and it’s called upon for them to go in a game, I don’t feel like they’re underprepared. I think they’re prepared to go in in those situations. We’ve obviously lost a couple people here early in these first three games. But it’s no different. Every team is dealing with injuries. In San Francisco, Vernon was out. They lost one of the best tight ends in the league. I think everybody just has to make adjustments as you go.

Q: How important is an athletic center, Jason Kelce, in what you guys do on offense?

KELLY: It’s part of what we do, and David Molk is an athletic center, also. He fits in the same mold as Kelce. We’re always looking for some athleticism in there at that position.

Q: What did you see from Nick Foles these first three games of the season in terms of second-half comebacks?

KELLY: What I’ve known all along. That Nick’s a gamer and that Nick is an unbelievable competitor. I got a chance to see his toughness when I faced him in college. I think people are just getting a chance to see it now. You always have a shot when he’s pulling the trigger.

Q: Could you talk about the emergence of Jordan Matthews in this past Sunday’s game?

KELLY: We thought – not thought – we knew what Jordan was capable of doing. A lot of what happens to us offensively just depends on how people defend us. You’ve got to try to take one aspect away or another aspect away – take our outside receivers away or our inside receivers or our tight end or our running back. But we feel we have weapons at all of our positions offensively. We’ve got figure out as the game goes along and make adjustments depending on how defenses are facing us. There’s a reason we drafted Jordan where we drafted him. He was very, very high on our board. We wanted to get bigger at the wide receiver spot, especially in the slot, thought it would create some good matchups for us and it’s paying off for us.

Q: I know you’ve said you’re not doing anything the NFL hasn’t seen before. Obviously some people in the media and otherwise have said you’re an innovator and changing the way things are done in the NFL. What are people pointing to when they say that?

KELLY: I don’t know. The Buffalo Bills ran an up-tempo offense. Tom Brady has run an up-tempo offense. The Cincinnati Bengals back in the day with Sam Wyche ran an up-tempo offense. Peyton Manning has done it throughout his career, whether he was in Indianapolis or Denver. So that’s what I say it, because it’s true.

Q: You said that Jim Harbaugh and Greg Roman scheme the run game really well. Can you talk about your history with them and maybe offseason visits to go over schemes?

KELLY: Yeah, just two guys I’ve got great respect for. Greg has come up to visit when I was at Oregon and they went to the 49ers. Obviously when they were at Stanford and we were at Oregon we didn’t share any notes on anything. But when they got to the league, Greg came up once and visited with us and we shared ideas. And then I had an opportunity during an open date when I was at Oregon in the season to go down and visit with those guys. Two guys I’ve got great, great respect for. Two really good football coaches.

Q: Did you get a lot of coaches come up there?

KELLY: We had a lot of guys want to come up but we only had a few come in.

Q: Meaning only a few followed through or only a few you allowed to come in?

KELLY: It only fit a few people’s schedules in the time we had available.

Q: Do you see the 49ers and Greg Roman using aspects of what you did at Oregon?

KELLY: Yeah I think they’ve run some zone-read stuff with Kap. They do a really good job of it. They’ve added their own wrinkles to it. I don’t think when anybody visits anybody they say, “Hey, I’m going to take this exactly from them.” I think you learn and then you think, “How can I apply it to the personnel I have?” And I think that’s one of the strengths of Jim and Greg is, is that they adapt their offense to their personnel.

Q: Are you surprised that LaMichael James is a free agent now, hasn’t found a team at this point?

KELLY: Yeah, I think LaMichael is a hell of a football player. I think maybe the timing had something to do with it because people’s rosters may have been set. I know him firsthand. I had an opportunity to coach him. I love the kid. He’s an awesome football player; he’s an awesome person.

Q: Is that the case with the Eagles? I know the 49ers tried to trade him earlier this year but you guys had already bulked up your roster at that position. Is that why Philadelphia ultimately wasn’t interested?

KELLY: I was unaware about anybody ever contacting us to trade anybody. But I feel very confident with LeSean McCoy and Darren Sproles and Chris Polk. We’ve got three backs active. Chris returned a kickoff for a touchdown for us last week. Obviously everyone knows what Darren and LeSean can do. I look at our running back position as a position of strength for us.

Q: Is what Zach Ertz doing about what you expected when you drafted him?

KELLY: The one thing about Zach is just how versatile he is, his ability to play tight end, his ability to line up in the slot, his ability to line up at wide receiver. You can line him up on a lot of different spots and they did at Stanford, both when Jimmy was there and when David Shaw was there. They’ve produced some really good tight ends at Stanford. What Zach is doing in the NFL is similar to the success he had at Stanford.

Q: Much was made of his short arms. Did some of his measurements give you a pause?

KELLY: I was unaware that he had short arms. They’re long enough to catch a football because he does a really good job of that.

Q: Nick Aliotti described your approach to running a football organization as science over tradition in terms of how you look at everything from practice to training to monitoring sleep of your players. Do you think that’s an accurate way to describe how you look at the world?

KELLY: The world?

Q: The football world.

KELLY: The football world? I’ve always been a person that questions, “Why?” If something has been done in the past – I guess Nick is speaking toward the tradition part of it – I would just ask, “Why?” And there are a lot of times when the why is explained to me and I say, “That makes great sense, we will continue to do it that way.” But the one thing I’ve never accepted is when the answer is, “That’s the way it’s always been done.” Give me a better reason than that, like if there are hard facts of this is why it’s supposed to be done this way. There are a lot of things when I question and get the answer I’m like, “Ah, that’s a really good answer, we’ll continue to do that.” I think everybody evolves. You go back 50 years ago, you weren’t allowed to have water at practice. And if you had water you were soft. I think people smartened up and learned the science behind hydration and things like that. Again, I don’t think we’re on the cutting edge of that. I think we emphasize what we think is going to put our players in the best position to be successful on Sunday.

Q: Getting back to tight ends and Zach Ertz, are tight ends something you are using more of in the NFL than you had as a college coach?

KELLY: No. We had great success in college. Ed Dickson, who’s still in the league, was an All-Pac-12 tight end when we were at Oregon. David Paulson who was just with the Steelers and has been in the league was an All-Pac-12 tight end. We’ve always been a tight end operation.

Q: I was just wondering, obviously the 49ers picked up some things from you guys. Does it work the other way? Have you picked up things from Harbaugh and Roman and the Stanford program and the 49ers there in Philadelphia?

KELLY: Yes, I’m an information gatherer.

Q: Can you be specific? Anything you can point to?

KELLY: Not off the top of my head.

Q: I know that you and the Eagles’ website will break down plays and go over film. In the NFL, a lot of coaches wouldn’t dream of doing such a thing. Do you think you’re relatively open as far as what you share because you don’t think it’s necessarily revolutionary? Is that accurate?

KELLY: No, I think other people do it. I’ve seen Bill Belichick. I’m from New England originally and they’ve had the Beli-strater for a long time. I don’t think that’s anything new to the NFL.