Re: The status of ID and a personal reflection

On Sat, 8 Mar 2025 2:31:58 +0000, RonO wrote:

On 3/7/2025 4:50 PM, Ernest Major wrote:

On 23/02/2025 21:52, MarkE wrote:

On 24/02/2025 6:10 am, Ernest Major wrote:

On 23/02/2025 11:43, MarkE wrote:

ID is described as "a pseudoscientific argument" on Wikipedia [1],
there's clearly no love for it here, and as far as I know ID has
limited recognition within mainstream science. The general public's
awareness and support of ID I believe is higher but still constrained.
>
ID has been accused of being a creationism Trojan Horse, and at
times it seems to have pursued a political agenda, especially with
education.  From to time to time, the Discovery Institute and
Evolution News promote a misplaced right-wing perspective.

>
In principle Intelligent Design could have been a legitimate
scientific research program, albeit one that I would not expect to be
productive. In practice it's a religiously motivated political movement.
>
ID's studied agnosticism (when not addressing a friendly audience)
about the identity and nature of the designer or designers is what
makes it clear that it's not a scientific research program. A
scientific research program would asking be who, what, why, when,
where and how, or at the least how to investigate who, what, why,
when, where and how.
>
The aim of science is to explain (if you're a philosophical realist)
or model (if you're a philosophical anti-realist) the world. By
eschewing questions of who, what, when, why, where and how, what ID
does is explain away observations, not explain them.

>
Noooooooooooo. You're ignoring the asymmetry I describe below. With
respect to a scientifically inferred designer, questions of who, what,
when, why, where and how are the province of theology, philosophy,
experience etc. In this context, science functions as a prompt and
pointer to other epistemological domains.

>
The Intelligent Design Movement didn't have to eschew questions about
the identity and properties of the design; that was a deliberate choice
made for political reasons.
>
Arguably they've slipped up on occasion, and let their unstated
assumptions leak into their arguments. They can't disprove evolution by
the absence of junk DNA anymore than they can disprove evolution by its
presence. I'm not old enough to remember the change, but as I understand
the history the existence of DNA was rather a surprise; it had been
naively assumed that natural selection would eliminate it. There remains
a widespread reluctance to accept its existence among biologists; few
would still defend an absolute panadaptationism, but panfunctionalism
doesn't seem to have received the same critical scrutiny.

>
Where the populations are large enough with a high reproduction rate
bacteria have been able to limit the amount of junk DNA.  They still
have to deal with some transposable elements and provirus inserted into
their genomes, but compared to eukaryotes they do a far better job at
dealing with transposons and viral sequences in their genomes.  40% of
the human genome was found to be due to interspersed repetitive elements
(transposon sequences and retroviral sequences) by the old DNA
hybridization tech, but this old technology could only match sequences
with at least a 75% sequence similarity.  Probably at least an equal
amount of genome sequence is ancient transposon sequence that has
mutated to the extent that they no longer cross hybridize.  Birds have
genomes only around 40%% the size of humans and have around the same
number of functional genes, but they have a lot fewer transposon
sequences.  They have been able to better control transposon numbers
than mammals, and it may not be due to flight.  Dinos and other reptiles
may have had genomes as small.  Fish like fugu have had the most luck at
controling transposon sequences and have only a 0.4 Gb genome while
humans with about the same number of genes has a 3.0 Gb genome.

Just to emphasize, the cost of carrying junk DNA just isn't
large enough for natural selection to keep it low ---
Except, for cases where reproduction speed is critical and
the total length of the genome is rate limiting.
To be clear, if 5% more DNA means it takes 5% longer for a cell
to reproduce, that is a large difference and natural selection
can be effective at increasing the relative population of a
variant that reproduces 5% faster when environmental conditions
allow for sustained population blooms. For that, 5% is a
very large effect.
In contrast, while 5% more DNA means 5% larger energy costs for
just the DNA replication part of metabolism, that is still a very
minor part of a cell's overall metabolism budget and so it just
doesn't rise to a threshold of significance for NS to be effective.
The more subtle aspect of this is that the "choice" of removing
Junk isn't some simplistic balance between a state where there is
some percent of Junk and one where all the junk has been surgically
removed by some very aware agent. It's a choice between wild-type
and a variant where some junk has been added or deleted. And
that will typically be a much smaller percentage than my cartooned
example of 5%.
The upshot is that the metabolic differential (energy cost) is
effectively even less and so even more insignificant in terms of
selection coefficients. But on the reproduction speed front, even
0.2% can make a difference.
The student is encouraged to play with generation times over 20
generations but should first review how to calculation compound
interest.

The ENCODE conclusion about having 80% of the genome as functional
sequence was stupid because they understood that they were counting
transposon sequence that have their own transcriptional regulatory
sequences, and transposons are mainly just DNA parasites.  Like any
other mutation most of the time a transposon jumps to a new position in
the genome not much happens to the organism, but sometimes something bad
happens (a lot of the dominant spontaneous deleterious mutations
identified in humans are due to transposons), and there can be rare
occasions where something interesting might happen and the event is
selected for.

ENCODE was stupid for many reasons. I prefer to explain  that they
conflated things that could be measured in their assays for things
that were functional. There assays were designed to look for some
of  the things that are known to have function. Then they assumed
their conclusion that the things they found must be functional.
In other words, they simply ignored or waved away the possibility
(likelihood) that there would be false positives in their assays
respective to function. I'm not saying they ignored the possibility
of false positives respective to the reproducibility of  their
assays. There, they at least worked to do a good job. Instead,
and again, they conflated being reproducibly detected in an assay
with being necessarily function. It smells of pan adaptionism
but it's possibly a more fundamental error.