I'll start this with my analysis of the text, then your questions and my answers at the end.
The following is the Dalai Lama's point of view, as explained in the article you referenced:
Science at the Crossroads
By Tenzin Gyatso, the Dalai Lama
This article is based on a talk given by the Dalai Lama at the annual
meeting of the Society for Neuroscience on November 12, 2005 in Washington DC.
He (Tenzin Gyatso, the Dalai Lama) as a scientist:
....The specific areas of science I have explored most over the years
are subatomic physics, cosmology, biology and psychology. For my
limited understanding of these fields I am deeply indebted to the
hours of generous time shared with me by Carl von Weizsacker and the
late David Bohm both of whom I consider to be my teachers in quantum
mechanics, and in the field of biology, especially neuroscience, .....
....which initiated the Mind and Life conferences that began in 1987
at my residence in Dharamsala, India. These dialogues have continued
over the years and in fact the latest Mind and Life dialogue concluded
here in Washington just this week.
Him as a religionist:
..Since the primary motive underlying the Buddhist investigation of
reality is the fundamental quest for overcoming suffering and
perfecting the human condition, the primary orientation of the
Buddhist investigative tradition has been toward understanding the
human mind and its various functions. The assumption here is that by
gaining deeper insight into the human psyche, we might find ways of
transforming our thoughts, emotions and their underlying propensities
so that a more wholesome and fulfilling way of being can be found. It
is in this context that the Buddhist tradition has devised a rich
classification of mental states, as well as contemplative techniques
for refining specific mental qualities.
..Some might wonder "What is a Buddhist monk doing taking such a deep
interest in science? What relation could there be between Buddhism, an
ancient Indian philosophical and spiritual tradition, and modern
science? What possible benefit could there be for a scientific
discipline such as neuroscience in engaging in dialogue with Buddhist
contemplative tradition?"
The two trends - a part, and a whole (a soul, and a stream):
... both Buddhism and modern science share a deep suspicion of any
notion of absolutes, whether conceptualized as a transcendent being,
as an eternal, unchanging principle such as soul, or as a fundamental
substratum of reality.
The Goal - (Paradigm Shift):
...complex world of inner subjective experience that we call the
mind...the effects of mental training, such as simple mindfulness
practice on a regular basis or the deliberate cultivation of
compassion as developed ....that mental practice can effect observable
synaptic and neural changes in the brain ....the deliberate
cultivation of compassion can lead to a radical shift in the
individual's outlook,
What is Paradigm shift? World and beyond the world (Change in Outlook):
...I am not advocating a fusion of religious ethics and scientific
inquiry. Rather, I am speaking of what I call "secular ethics" that
embrace the key ethical principles, such as compassion, tolerance, a
sense of caring, consideration of others, and the responsible use of
knowledge and power - principles that transcend the barriers between
religious believers and non-believers, and followers of this religion
or that religion.
Problem domain - (world within):
..do individuals have a fixed capacity to regulate their emotions and
attention or, as Buddhist tradition argues, their capacity for
regulating these processes are greatly amenable to change suggesting
similar degree of amenability of the behavioral and brain systems
associated....
Solution domain - (beyond the world):
..modern neuroscience has developed a rich understanding of the brain
mechanisms that are associated with both attention and emotion.
Buddhist contemplative tradition, given its long history of interest
in the practice of mental training, offers on the other hand practical
techniques for refining attention and regulating and transforming
emotion...the cultivation of a compassionate heart and the cultivation
of deep insights into the nature of reality, which are referred to as
the union of compassion and wisdom.
The difficulty is searching for solutions within the world; but the solution is beyond the world. So only the path can be shown, not the end result. (It should be taste and see).
Path? or Paths? (Or suits?):
...in its traditional context, the term for meditation is bhavana (in
Sanskrit) or gom (in Tibetan).
..The assumption here is that by
gaining deeper insight into the human psyche, we might find ways of
transforming our thoughts, emotions and their underlying propensities
so that a more wholesome and fulfilling way of being can be found...
At the heart of these meditation practices lie two key techniques, the
refinement of attention and its sustained application on the one hand,
and the regulation and transformation of emotions on the other...
Broadly speaking, there are two categories of meditation practice -
one focusing on stilling the mind and the other on the cognitive
processes of understanding. The two are referred to as (i) stabilizing
meditation and (ii) discursive meditation.
Who has gone?
... insofar as empirical facts are concerned, facts must remain facts,
no matter how one may choose to describe them. Whatever the truth
about the final nature of consciousness - whether or not it is
ultimately reducible to physical processes - I believe there can be
shared understanding of the experiential facts of the various aspects
of our perceptions, thoughts and emotions.
So Now the Q & A.
- With specific reference to the last line: in the "Buddhist investigation of reality", what are the instances where empirical
evidence "should triumph over" (or even challenge) scriptural
authority?
Traditional cosmology ( IF found in ) ancient Buddhist texts. But It
cannot compare cosmology and Buddhist 31 planes each other.
- Are there alternative/contradictory points of view in the scriptures, or in the talks and writings of recent Gurus, to the Dalai
Lama's point of view (i.e. wherein it is posited that scriptural
authority should prevail over empirical evidence)?
There is no Scriptural authority in Buddhism. (As shown in "Kalama
Sutta"). Empirical evidence and other facts found in ancient Buddhist texts are
used as "Uppaya". Like "finger" to point the "Moon".
