please empty your brain below

I'd argue it's the other way around, the padding is to aid co-ordination with the outer sections (east of Stratford, west of Paddington) where more random stuff can go wrong.

This is also the computer controlled section, which might be a factor - is it the same on computer controlled section of Thameslink.
Whilst padding is a factor, a more significant point is that trains (Underground and Elizabeth line) are so fast between stations because of automatic train operation. Before that better acceleration ability in more modern stock made a significant difference from the opening of the Victoria line onwards. In this sense the 'problem' will get worse on the Underground (and eventually National Rail in London) as trains spend less time between stations.

The lack of sharp curves on the Elizabeth line (and hence the lack of speed restrictions) is also very significant.

As a rough guide to estimate your journey time, allow two minutes between stops on the Underground in the central area. This also applies to the Elizabeth line. Dwell time at stations, especially with platform edge doors, is inevitably a significant part of the journey time. Add acceleration and deceleration from and into stations and the actual distances between stations is almost irrelevant. A significant portion of this time is spent slowing down, stopping and accelerating out of stations.
'Chavtartan Street' just perfect
Last I heard the Circle line doesn't go to Whitechapel (apart from those special early morning movements). Did you mean the H&C?

dg writes: yes, sorry.
The dwells at the station formerly known as Bond Street seem rather short in comparison to the others. The station can't be that much less busy.
Some of the station stops outside the central area also seem excessively long. Travelling into London on the Shenfield arm of Crossrail, the station stop at Stratford is nearly always in excess of 60 seconds. There is some logic in this as it means that trains should (in theory) be on time as they approach the central section at Whitechapel and merge with the Abbey Wood branch. However, there doesn't seem to be any logic in having lengthy dwell times once in the central section itself.
It would be interesting to compare journey times if they cranked it up to Victoria Line levels of persistent urgency.

I wasn't impressed with the information system during delays last week. The departure screens upstairs showed trains coming through every few minutes but subject to delays, but on the platforms the screens displayed the delay message without any information on the next trains, so no one knew the destination until boarding.
I spent some time working on dwell times in a similar section of a different metro system. As a general principle, it's best not to have trains stopping between stations, as you're wasting energy stopping and starting, and it's also a major problem if there is a serious problem ahead and the train has to be evacuated. So you don't despatch a train from one station until you are pretty sure the train ahead will have left the next station before you arrive. That also means that while you're waiting, newly arrived passengers can board. In the Eliz line case, I would guess that a major factor is the dwell time needed at Paddington (westbound) to cope with its interchange volume, which - because of the above - will impact the dwell time at the earlier stations.
You’d like your already quite fast (compared to walking or driving or other public transport) train ride to be one minute faster. Welsh drivers are being asked to accept that their car journey will be one minute slower.

Is either really a problem, or just an interesting observation?

Unlike the blue abomination at Chavtartan Street, which really is a problem. TfL seems to think it is acceptable to deliberately confuse and inconvenience its customers, if someone pays them enough to do so.
The technical definition of dwell time (as DG hinted at) is wheel stop to wheel start to include the ‘useful’ portion of dwell when the doors are open and passengers and board / alight and the not useful portion when the various systems are talking to each other to confirm it is safe to open the platform edge and train doors.
It seems pointless to guzzle lots of power to massively speed up the train, then slow down... I realise that regenerative braking is used to collect a major part of this energy, but it's not 100% efficient, so why not just go a little slower???
The dwell times give some flexibility to synchronise with the main line trains at each end, and it is probably better to even tyhem out over the central section than have the trains rush to Paddington/ Whitechapel and then hang around waiting for time (inevitably holding up a following train in a tunnel)
If you think those dwell times are long, try a trip on a LNWR train. No sensors to detect where the train has stopped, or reliance on the driver stopping at the correct position. Instead the guard gets off at every stop, looks up and down the train to check that it is entirely at the platform, gets back on and only then enables the door open buttons (which work painfully slowly). I think they must be trying to make a case for the driver opening the doors.
Presumably it takes some time to ensure that trains terminating at Paddington are empty, impacting the time at other stops. In fact i am surprised they can do it that quickly.
It is odd that dwells as so long. One of the defined outputs of the Thameslink programme was that dwells could be 40 seconds long, stop to start.

Not sure about the comments about synching with the lines at each end - the dwells are consistent and timetabled, so there's no obvious reason the train couldn't be timetabled for different dwell times.
It does seem timetabled for a hypothetical massive flow of passengers at each station. Likely coupled with the need to terminate trains at Paddington which seems to be a major handicap (iirc the auto train reversal needed to maintain short headways despite a terminus there caused numerous issues). The service does seem to bunch up though quite regularly despite this. Funny sometimes that this is shown by trains on the next train display 'overtaking' one another in the Central Core though obviously this is physically impossible.
My understanding is that the extended dwell times were introduced initially 'just in case' so as not to stress the timetable too much on what was already a problematic scheme. They will hopefully get cut down a bit in future iterations of the timetable.

One issue with them which is unlikely to be solved is that in theory National Rail working time tables (Elizabeth Line being an NR service) only have resolution down to 1/2 minutes - so it's either 30 or 60 seconds, where 40 seconds might generally be appropriate at most COS stations.
The standard timetabling dwell time allowances for Crossrail are 30 seconds for Station calls (not terminating), and 60 seconds for Passenger service to ECS with no change of direction (e.g. at Paddington).
Dwell times are to protect and ensure the headway is maintained within the Central Operating Section, nothing more, nothing less.

If a dwell is reduced, this isn’t done by the driver, it’s automated by the signalling system which is attempting to catch the train back up to the right time in timetable.

This is why a train can open doors at a station and then immediately close them, because the system is aiding the train to reduce its dwell, a train can be late at Paddington and then be back to normal 60 sec dwells at Canary Wharf because the delay has reduced through this method.

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