Tuesday, December 19, 2023
World-First Human Brain Atlas Reveals New Cell Types
Thursday, November 23, 2023
Against "Junk DNA"
Newly Published Paper in BioEssays Recognizes
Kuhnian “Paradigm Shift” Against Junk DNA
November 22, 2023, 7:44 AM
September, I wrote about
prolific functions discovered for short tandem repeats (STRs), formerly
considered a type of “junk DNA.” Now a newly published paper in BioEssays has
strongly rebuffed the idea of junk DNA — using the language of Kuhnian paradigm
shifts. Before we go any further, let’s review just what a Kuhnian paradigm
shift is.
The phrase comes from the work of a famous Harvard University historian
and philosopher of science, Thomas Kuhn. In his
influential book The Structure of
Scientific Revolutions, he documented how new ideas in science
typically take hold through what are called “paradigm shifts,” where the
leading framework within a field (the “paradigm”) starts to accrue evidential
problems (goes into “crisis”) until it finally gives way to a new idea that
challenges the status quo. Kuhn further showed that most scientists spend most
of their time doing “normal science” — basically solving scientific puzzles
within the framework of the dominant paradigm. He observed that the scientists
of the old guard paradigm are “often intolerant” of “new theories” that are
being proposed by new scientists proposing ideas that challenge the reigning
paradigm. A new theory “emerges first in the mind of one or a few individuals”
but then it spreads because the field faces “crisis-provoking problems,”
especially among scientists who are “so young or so new to the crisis-ridden
field that practice has committed them less deeply than most of their
contemporaries to the world view and rules determined by the old paradigm.”
A Junk DNA Paradigm Shift
This brings us to the article recently published in BioEssays,
written by John Mattick, an Australian molecular biologist and Professor of RNA
Biology at the University of New South Wales, Sydney. I have no evidence that
Mattick has any affinities with intelligent design — but he’s a prime example
of a bold scientist who has embraced new theories that challenge the reigning
paradigm. Mattick has been indefatigable in following the evidence where it
leads regarding evidence of function for “junk DNA.” In part because of his
work, biology today has experienced a paradigm shift away from the concept of
junk DNA. In fact, Mattick’s new BioEssays article, “A Kuhnian
revolution in molecular biology: Most genes in complex organisms express
regulatory RNAs,” frames the revolution in thinking over junk DNA
precisely in “Kuhnian paradigm shift” terms. The paper has a nice video abstract, but here’s
what it says in written form:
Thomas Kuhn described the
progress of science as comprising occasional paradigm shifts separated by
interludes of ‘normal science’. The paradigm that has held sway since the
inception of molecular biology is that genes (mainly) encode proteins. In
parallel, theoreticians posited that mutation is random, inferred that most of
the genome in complex organisms is non-functional, and asserted that somatic
information is not communicated to the germline. However, many anomalies
appeared, particularly in plants and animals: the strange genetic phenomena of
paramutation and transvection; introns; repetitive sequences; a complex
epigenome; lack of scaling of (protein-coding) genes and increase in
‘noncoding’ sequences with developmental complexity; genetic loci termed
‘enhancers’ that control spatiotemporal gene expression patterns during
development; and a plethora of ‘intergenic’, overlapping, antisense and
intronic transcripts. These observations suggest that the original conception
of genetic information was deficient and that most genes in complex organisms
specify regulatory RNAs, some of which convey intergenerational information.
Mattick describes the previously reigning “junk DNA” paradigm in biology
as having come from “prevailing assumptions.” The assumptions hold that
“‘genes’ encode proteins, that genetic information is transacted and regulated
by proteins, and that there is no heritable communication between somatic and
germ cells.” This view that genes encode proteins is a key part of the “central
dogma” of biology. Of course, no one denies that genes encode proteins —
Mattick’s point is that they can do much more than this. They can also encode
RNAs and the evidence shows that many non-protein-coding sequences of DNA
actually encode RNAs that perform many types of vital functions in the
cell.
Junk DNA and Evolution
So the central dogma of molecular biology is part of what is
perpetuating the idea that if a stretch of DNA doesn’t encode a protein then it
isn’t doing anything and is “junk.” But there’s another major driver of the
failing junk DNA paradigm in biology — and it stems directly from evolutionary
thinking. Mattick explains:
[T]heoretical biologists were
integrating Mendelian genetics with Darwinian evolution, leading in 1942 to the
so-called Modern Synthesis, which made two primary claims: mutations are random
and somatic mutations are not inherited. … In 1968 Kimura proposed the neutral
theory of molecular evolution, which posited that “an appreciable fraction” of
the genome was evolving independently of natural selection. In 1969, Nei
concluded that, given the “high probability of accumulating … lethal
mutations in duplicated genomes … it is to be expected that higher organisms
carry a considerable number of nonfunctional genes (nonsense DNA) in their
genome”, leading Ohno to promote the concept of “junk DNA”,
also arguing that “in order not to be burdened with an unbearable
mutation load, the necessary increase in the number of regulatory systems had
to be compensated by simplification of each regulatory system”. [Emphasis
in the original.]
Against this backdrop — permeated with evolutionary
thinking about the origin of the genome — the idea of junk DNA flourished and
spread throughout the biology community.
Wednesday, October 11, 2023
GPT4 is utterly incapable of reasoning
Sunday, September 10, 2023
The Lotus Sutra is not a counter-example to the Kuzari Principle
A National Experiential Tradition is defined as:
1) a
tradition accepted by a nation about its own history
2) a tradition that
describes a national experience of a previous generation of that nation
3) a national
experience that would be expected to create a national memory that would continue until the time
when the tradition is in place.
The Kuzari principle says that national experiential
traditions are true.
Some critics think that the events described in the
Buddhist Lotus sutra are a counter
example to the Kuzari principle. Here I will show that those events do not
satisfy the definition of an NET and therefore are not counterexamples to the
Kuzari principle.
Here is a summary of the four main ways in which those
events fail to meet the condition of the of the of the definition:
A, It is not clear that the events describe large
scale human participation at all. Many of the beings described are clearly not
human. Even when human terms are used, the numbers are clearly symbolic and not
literal. That creates the impression that there is no description of a real
human historical event. [So 2) is
violated since a national event is a large scale human event.]
B. Even if we took the description to refer to large
scale human participation, there is no description of the human group constituting
a nation who could be the ancestors of a nation that possessed the tradition
describing the events. See my discussion of the battle of the Milvian bridge in
Reason to Believe pp. 272 - 274 for the significance of lacking national
identity. [So 1) and 2) are violated.]
In addition, the Lotus sutra originated in a culture
distinct from the descendants of the supposed original event.
According to the New World Encyclopedia (https://www.
The Lotus Sutra was published in
Kashmir (or Punjab) during the Kushan dynasty, under king Kanishka´s reign. The
Kushan dynasty was a different civilization than the Haryanka dynasty (that
is king Ajātaśatru´s dynasty, who was allegedly present with his
people when the Buddha performed the miracles).
As you know, one key component of
the Kuzari Argument is (2) a national experience of a previous generation of
that nation; that´s because if a relevant enough event happened, it should
have left a memory on that nation as a whole, and that makes it verifiable.
It seems that the sutra doesn’t
meet this requirement because this book was published by a nation that wasn´t
the same nation where the miracles allegedly happened, and therefore the
verifiability of the event fades away.
If someone in the Kushan empire
asked “how come anybody knows about it” the fourth council would reply, “that´s
because it didn´t happened to us, it happened to a different people and those
people aren´t here” that means it´s unverifiable and therefore the Kuzari
argument would not apply to the Lotus Sutra.
This crucially
violates 2). My thanks to Marcus Rayek for this crucial information.
C. The Lotus sutra is revered only by one of the three
major branches of Buddhism, namely Mahayana. That means that it's authority as a direct
revelation from God it's not accepted by the other two schools, namely Theravada and Vajrayana. That means that the
veracity of the historical event is rejected by a large portion of the of those
who are faithful to Buddhist tradition. That suggests that even in Mahayana it was not regarded as
historical fact, but rather as a poetical exposition of fundamental beliefs and
practices with which the other two branches somewhat disagreed, rather than a
disagreement about an event of revelation. That being the case, the description
of the historical events in the Lotus sutra cannot be regarded as a tradition accepted
by a nation about its own history. [So 1) is violated.]
D. The date of origin of the Lotus sutra is very much
in doubt. Here are the words of one of the translators of the sutra [https://www.academia.edu/36790850/Tracing_the_progressive_definition_of_the_Bodhisattva_Avalokite%C5%9Bvara_in_imagery_and_textual_discourses]:
We do not know where or when the
Lotus Sutra was composed, or in what language. Probably it was initially
formulated in a local Indian dialect and then later put into Sanskrit to lend
it greater respectability. All we can say for certain about the date of its
composition is that it was already in existence by 255 ce, when the first
Chinese translation of it was made.
From another source [https://tricycle.org/magazine/how-to-read-the-lotus-sutra/]:
The Lotus Sutra was
probably compiled in the first century C.E. in Kashmir, during
the fourth Buddhist Council of the newly founded Mahayana sect of Buddhism,
more than 500 years after the death of Sakyamuni Buddha [1] It is thus not
included in the more ancient Agamas of Mahayana Buddhism, nor in the
Sutta Pitaka of the Theravada Buddhists, both of which
represent the older Buddhist scriptures that can be historically linked to Sakyamuni Buddha himself.
Given that date for its composition, we can either say
it is meant as a literal history and comes into existence in violation of the Kuzari
principle, or we can say that it is meant as poetry - and not as literal history
- and does not violate the principle. There is no convincing reason that we
should opt for the former over the latter. [So 1) is violated.]
[[More support for this conclusion is fund in the
following quote from the first source above:
In these
opening sentences we are still in the world of historical reality or
possibility, in a setting in the outskirts of the city of Rajagriha in northern
India in which Gautama, or Shakyamuni, very probably did in fact propound his
doctrines in the sixth or fifth century bce.
But as
Ananda proceeds to describe the staggering number and variety of human,
nonhuman, and heavenly beings who have gathered to listen to the Buddha’s
discourse, we realize that we have left the world of factual reality far
behind. This is the first point to keep in mind in reading the Lotus
Sutra. Its setting, its vast assembly of listeners, its dramatic
occurrences in the end belong to a realm that totally transcends our ordinary
concepts of time, space, and possibility. Again and again we are told of events
that took place countless, indescribable numbers of kalpas, or eons, in the
past, or of beings or worlds that are as numerous as the sands of millions and
billions of Ganges Rivers. Such “numbers” are in fact no more than
pseudo-numbers or non-numbers, intended to impress on us the impossibility of
measuring the immeasurable. They are not meant to convey any statistical data
but simply to boggle the mind and jar it loose from its conventional concepts
of time and space. For in the realm of emptiness, time and space as we
conceive them are meaningless; anywhere is the same as everywhere, and now,
then, never, forever are all one.]]
In addition, other contradictions and historical
problems are pointed out below.
THE LOTUS SUTRA
Chapter I
Introduction
[Text in italics is my addition of historical information.]
Thus have I heard. Once the Buddha was staying in the
city of Rājagṛha, on
https://www.oxfordreference.com ›
view › authority.2...
The capital of Magadha until
the end of the Haryaṇka dynasty. Built by King Bimbisāra,
https://www.oxfordreference.com ›
viewbydoi › auth...
Founder of the Haryaṇka dynasty and first king of
Magadha.which he ruled for 52 years (c.465–413 bce) from his palace in Rājagṛha.
So the city was built no earlier than 465
B.C.E. This date is consistent only with the latest dates for Buddha’ life. According
to the earlier dates these events could not have happened in his lifetime.
the mountain called Gṛdhrakūṭa, together with a great assembly of twelve
thousand monks, all of whom were
arhats whose corruption was at an end,
who were free from the confusion of desire, who had
achieved their own
goals, shattered the bonds of existence, and attained complete
mental discipline.
Their names were Ājnāta kauṇḍinya, Mahākāśyapa, Uruvilvakāśyapa,
Gayā kāśyapa, Nadī kāśyapa, Śāri putra, Mahā maudgalyāyana, Mahā kātyā -
yana, Aniruddha, Kapphiṇa, Gavāṃ pati, Revata, Pilinda
vatsa, Bakkula,
Mahā kauṣṭhila, Nanda, Sundarananda, Pūr ṇa maitrā yaṇī putra, Subhūti,
Ānanda, and Rāhula.
20 names for 12,000 monks.
All of them were great arhats, known to the assembly.
There were in addition two thousand others, both those
who had more to
learn and those who did not. The nun Mahā prajāpatī was there, together with
her six thousand attendants; and also the nun Yaśodharā, Rāhula’s mother,
together with her attendants.
There were also eighty thousand bodhisattva mahā sattvas, all of whom
were irreversible from highest, complete enlightenment (anuttarā samyaksaṃbodhi).
They had obtained the dhāraṇīs, were established in eloquence,
and had turned the irreversible wheel of the Dharma. Each
had paid homage
to countless hundreds of thousands of buddhas, planted roots of merit
in their
presence, and had always been praised by those buddhas.
“Countless” clearly contradicts “hundreds of
thousands”. In any case, it is clearly impossible for any real human being to
receive homage from hundreds of thousands of real human beings.
They had also cultivated
compassion within themselves, skillfully caused others to
enter the
wisdom of a buddha, obtained great wisdom, and reached
the other shore. All
of them were famous throughout countless worlds and had
saved innumerable
hundreds of thousands of sentient beings. They were Manjuśrī, Avalo -
kiteśvara, Mahāsthāmaprāpta, Nityodyukta, Anikṣipta dhura, Rat na pāni,
Bhaiṣajyarāja, Pradānaśūra, Ratnacandra, Can dra prabha, Pūrṇa candra,
Mahāvikramin, Anantavikramin,
Trai lokya vikrama, Bhadra pāla, Maitreya,
Ratnākara, and Susātha vāha.
These are the names of all 80,000?!
There were altogether eighty thousand such
bodhisattva mahāsattvas.At that time Śakra, king of the devas,
Śakra (Sanskrit: शक्र Śakra; Pali: सक्क Sakka) is the ruler of the Trāyastriṃśa Heaven according to Buddhist cosmology. He is also referred to by the title "Śakra, Lord of
the Devas"
(Sanskrit: Śakra devānāṃ indraḥ; Pali: Sakka devānaṃ inda).[1] The name
Śakra ("powerful") as an epithet of Indra is found in several verses of the Rigveda.
Clearly
a mythological figure not human.
was also there, attended by twenty
thousand devaputras. Candra, Samantagandha, and Ratnaprabha,
and the
great devas of the four quarters were there, together with a
retinue of ten
thousand devaputras. The deva putras Īśvara and Maheśvara were there,
attended by thirty thousand devaputras. Brahma, the lord of
the sahā world,
as well as the great Brahma Śikhin and the great Brahma Jyotiṣprabha were
there, together with a retinue of twelve thousand devaputras. The eight nāga
kings
Who were the Naga kings?
Chronology
- Vrisha-naga alias Vrisha-bhava or Vrishabha, possibly ruled at
Vidisha in the late 2nd century. ...
- Bhima-naga, r. c. 210-230 CE, probably the first king to rule from
Padmavati.
- Skanda-naga.
- Vasu-naga.
- Brihaspati-naga.
- Vibhu-naga.
- Ravi-naga.
- Bhava-naga.
The Naga (IAST: Nāga) dynasty ruled parts of north-central India during the
3rd and the 4th centuries, after the decline of the Kushan Empire and before
the rise of the Gupta Empire. Its capital
was located at Padmavati, which
is identified with modern Pawaya in Madhya Pradesh. Modern historians
identify it with the family that is called Bharashiva (IAST:
Bhāraśiva) in the records of the Vakataka dynasty.
So they
are approximately 500 years after the life of Buddha. So this reference to
human participation cannot be historically accurate.
—namely, Nanda, Upananda, Sāgara, Vāsukin, Takṣaka, Anavatapta,
Manasvin, and Utpalaka—were also
there, each of them surrounded by several
hundreds of thousands of attendants.
There were four kings of the kiṃnaras
A kinnara is a creature from Hindu and Buddhist mythology. They are described as part human and part bird, and have a
strong association with music and love. Believed to come from the Himalayas, they often
watch over the well-being of humans in times of trouble or danger. An ancient
Indian string instrument is known as the Kinnari vina.
So these
are mythological creatures.
whose names were Dharma, Su -
dharma, Mahādharma, and
Dharmadhara, and each had several hundreds of
thousands of attendants. The four kings of the gandharvas were there. They
were Manojna, Manojnasvara, Madhura, and Madhurasvara,
each of them
also with several hundreds of thousands of attendants.
There, too, were four
kings of the asuras,
Asuras (Sanskrit: असुर) are a
class of beings or power-seeking clans, related to the more benevolent devas (also
known as suras) in Hinduism.[1]
Since no names are mentioned, this is an
indefinite reference impossible to place historically.
called Baḍin, Kharaskandha, Vemacitra, and Rahu, each
with several hundreds of thousands of attendants. Mahā tejas, Mahākāya,
Mahā pūrṇa, and Maharddhiprāpta, the four kings of the garuḍas,
The Four Heavenly Kings are
four Buddhist gods
or devas, each of whom
is believed to watch over one cardinal direction of the world. In the Sanskrit language
of India, they are called the "Caturmahārāja" (चतुर्महाराज) or "Caturmahārājikādeva": "Four
Great Kings". In Chinese mythology, they are known
as "Sì Dàtiānwáng" (Chinese: 四大天王; lit. 'Four
Great Heavenly Kings') or collectively as "Fēng Tiáo Yǔ Shùn" (simplified Chinese: 风调雨顺; traditional
Chinese: 風調雨順; lit. 'Good
climate'). The Hall of Four Heavenly Kings is a standard component of Chinese Buddhist temples.
So the
four kings are clearly not human kings.
were there
together with several hundreds of thousands of
attendants. Finally, King
Ajāta śatru, Vaidehī’s son,
I find no historical reference for this person.
So the
bottom line is that all the references to the kings and their attendants are
references to mythological creatures except for one set of kings who are four
centuries too late. That means that the description of this being a large scale
public event is entirely unreliable.
was also there
with several hundreds of thousands
of his attendants.
Also notice that all the numbers are in round
thousands. There was no interest here in counting the number of actual
participants. The numbers indicate great multitudes and perhaps relative size.