SFT, TMR4A, and Created Heterozygosity

Any idea when/where you’ll publish on this?

Depends how some uncontrollable factors shape up. As you can imagine, this is not the easiest sort of work to place.

Is there a repo for any TMR4A-related code publicly available?

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Not at the moment. Do you have a plan you’d like to discuss? Even better, would you want to help us shape this into a paper? You’d get some authorship :slight_smile: .

Absolutely. I could envisage a “proper” scientific article describing the concepts and algorithms and discussing the utility of calculating various coalescence timeframes to different numbers of alleles to make inferences about population sizes, followed by a subsequent article in a slightly more theological setting (ASA?) going more into the Adam and Eve stuff. Just a idea, obviously it’s your decision and you’ve put a lot more thought into it.

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Oh gosh, It’s tempting, but I’ve already got multiple side projects I’m working on. And…oh yeah…a dissertation. For now, I’m going to politely decline. But if it’s still sitting around in a year and nobody else has picked it up, I might be interested

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Well, it’s a side hustle as you know. Pragmatically speaking, I need to know if you guys want to help out? If so, that will help things along immensely.

I don’t think there’s much point if SFT himself isn’t going to be involved or put in any effort. These kinds of debates are his day job, for me it’s a hobby I try and find time for. I’ve got much better things to do than respond to someone who can’t even be bothered to engage and try and present arguments coherently and completely.

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I mean, similar to Dave I’m massively busy at the moment, working on 5 projects, but I’m certainly willing to help speed things along where I can.

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Are you sure you know what gene conversion is? That really doesn’t sound sensible.

Not sure what the advantage is there. You need massive recombination within genes in order for this program to work. And it has to be a weird sort of recombination to produce the observed divergence within families, a sort of coordinated recombination that carefully assigns nucleotide site alleles to produce that divergence and also a nested hierarchy. In other words, God has to micromanage all the recombination. It would seem simpler just to micromanage mutations.

But you aren’t proposing that scenario. Let’s keep the number of miracles down; more sciencey that way.

I have no idea what you mean by that. Do you know what a lineage is?

True. It would seem that there’s way too much variation in both Y and mitochondrial chromosomes within kinds to fit this scenario. In fact, the Y chromosome evolves more rapidly than the autosomes, and you can’t call that created heterozygosity. Toss in the W chromosome in birds, butterflies, and other organisms with similar systems, and you have a serious problem for your scenario.

Sure. Any possible sequence can be assembled from a genome maximally heterozygous (all 4 bases) at every position. But is that biologically sensible? Would such a creature even be viable? I have doubts.

I did. I don’t think you know what gene conversion is. Read my responses carefully.

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I think it’s important to recognize that a subset of the audience is not interested in understanding and accurately representing the concepts in question. Communication to non-scientific audiences is something scientists need to do a lot more of, and work a lot more at, but not all members of that audience will be receptive. Lead a horse to water, etc.

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I see now that @SFT actually seems to agree that current recombination rates can’t make created heterozygosity work as an explanation for getting our current genetic diversity in 6000 years. Instead he suggests that God put the created heterozygosity in the genome such a way that special linkage groups would break variants up deliberately, and then presumably these linkage groups disappeared, i.e stopped recombining at all those specific intragenic locations, over time such that modern human show no trace of them. It’s a very convenient ad hoc fix to the problem, a literal “god did it” excuse.

At 23:30 in this video:

Why he refuses to explain himself concisely in text is beyond me though - we shouldn’t have to trawl through hours of rambling streams like this to pick up his claims.

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He seems to be invoking something much more akin to the germline diversity model in that Sanford paper than the CHNP model Jeanson espouses. But this is not at all clear.

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The reality seems far less coherent. He is mixing and matching and spinning tales.

The better approach is to define several models of a YEC AE and see which ones are ruled out and which ones are not ruled out. If we find one that is not ruled out, that isn’t a problem. Maybe there is a model that works, but we need to be clear about what that model is and what it demands.

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It doesn’t quite sound like that to me. Earlier in this thread he clarified that he didn’t think that germline model was required, to me it sounds like he’s going with Jeanson’s version of CHNP but adding in some kind of temporary recombination hotspots that were present early on in human history but undetectable today.

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Right, what he says implies the Jeanson CHNP model, with some unnatural P’s included as necessary. But then the paper he cites in support of his position does invoke created germline diversity. I’m not sure if he realizes there’s a conflict there, and he didn’t respond when I asked. @SFT, which model, if either, are you using here, and for the one you are using, are the any differences between “your” version and the “published” version?

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A lot of temporary hotspots. A whopping lot.

@evograd,

So he more or less confesses this approach at 23:30 in the video?

@evograd

Here is the raw transcript:

23:18
he says he says the rate of
recombination is
too slow to break all those different
variants
up to get so many different alleles

okay for one the question i would have
23:33
would be doesn’t gene conversion break
these up
faster and the answer is yes there’s
different processes other than
recombination of course
and it’s obvious that god would have
placed
assuming created heterozygosity god
would have placed
these design variants in useful linkage
groups
that’s the quick answer okay god and
that’s what’s funny that’s why they want
to pretend to assume created
heterozygosity
23:59
and then use an argument that assumes a
way created heterozygosity like this
argument
as if god just placed these design
variants
in adam and eve the biblical kinds but
then oops you know forgot to put them in
useful linkage groups they can’t break
apart

24:14
so that’s just silly god obviously would
24:16
have placed these design variants in
24:17
useful linkage
24:18
groups but we’re going to get a little
24:19
more technical anyways but that’s just
24:20
the the quick
24:22
the quick answer so i want to screen
24:24
share
24:26
a conversation that we were having
24:28
because
24:29
even dr frello was
24:33
corrected on this in jensen frelo
24:36
written debate
24:38
okay screen share
24:42
and admitted that he had the incorrect
24:46
incorrect definition of allele so it
24:48
looks like
24:50
dan is kind of now accepting the
24:54
tmr4a
24:57
position that i’m pointing out but now
24:58
he’s he’s pointing out the fact that
25:00
even with
25:01
the allele definition that we should be
25:03
using there’s going to be an issue
25:04
because those
25:05
variants cannot be broken apart
25:08
correctly so just one second so i’m
25:09
screen sharing
25:11
make sure it’s good i’m just gonna get a
25:13
drink of water
25:16
good to see everybody doki doki
25:21
faithful honest and true you’re late
25:25
better late than never though okay get a
25:28
drink here
25:33
all righty let’s go into here stacy
25:39
so i went heavily into this yesterday
25:43
and i’m still i’m going to challenge the
25:45
i’ve been using the the hat map data
25:47
fascinating data that suggests
25:50
biblical creation i’ve been using that
25:52
for months
25:53
use it in erica’s debate even how do you
25:56
can skip go to the third debate skip to
25:58
my final slide where i have a list of
26:00
questions broken down
26:01
um it’s funny she’ll say that you know i
26:05
i don’t
26:06
make it easy you know instead of
26:07
watching a two-hour video just break
26:08
down the questions i wanna answer well
26:10
it’s the same question six months ago
26:12
or four months ago whenever that debate
26:13
was time flies by linkage groups is one
26:16
of them hat map data is one of them so
26:18
um i’m i’m suspecting if dan didn’t even
26:21
want to engage the hat map data in the
26:23
lecture
26:24
then there’s probably no good answer out
26:27
there for
26:28
it from the evolutionary perspective
26:31
okay so there’s a lot of comments in
26:32
here you can go read it for yourself
26:35
here we go so i decided to jump in
26:37
because katherine’s stormguard actually
26:40
looked like she was being objective and
26:41
wanted an answer so therefore i didn’t
26:43
mind getting into this
26:44
instead of just a comment war where
26:46
someone’s not really looking for an
26:47
answer so
26:49
here’s what i said yes dan seems to have
26:53
adopted the improper definition of
26:54
allele
26:56
you’re right i did point this out in my
26:58
stream last night
27:00
but i hope dan deals with it in his
27:01
response he kind of did i guess but yeah
27:04
let’s
27:04
get into that firstly when it comes to
27:07
the hypervariable positions it is a fact
27:10
that some regions of the genome seem
27:11
more prone to mutations than others
27:14
okay let’s see well i’m going to point
27:17
out the fact too with what we now know
27:19
about epigenetics
27:20
and what goes on in the genomic in the
27:23
genomes of living biological organisms
27:25
we’ve got millions and millions of
27:26
switches
27:27
just ready and willing to be turned on
27:30
and off
27:31
based on environmental stimuli you know
27:34
there seems to be
27:35
genetic algorithms in our genome that
27:38
are built in to adapt
27:40
and we can see that there are various
27:42
genes that are only expressed under
27:43
certain conditions rna genes like
27:45
pseudogenes for example so
27:47
there’s a lot going on in the genome
27:49
that would suggest
27:51
that these genomic regions often times
27:54
the hypervariable regions the fact that
27:56
they’re more prone to mutations
27:58
more prone to adaptation but yeah
28:02
let’s get back to this so now the
28:04
correct
28:05
uh nicholas says epigenetics yeah we’re
28:07
going to be talking uh
28:10
we’re going to be talking a lot about
28:11
epigenetics on monday
28:13
with john sander with dr carter
28:16
nicholas so it’s gonna be a lot of fun
28:18
okay so i continue
28:21
i see now the correct definition of an
28:24
allele is
28:24
one of two or more versions of a
28:26
particular dna position
28:28
so here’s where they cornered themselves
28:31
you can watch a discussion i had with
28:33
uh speed of sound it was an hour
28:34
discussion just on alleles and the uh
28:37
definition for and he just wouldn’t
28:38
answer he wouldn’t give a straight
28:40
answer
28:41
because they contradict themselves with
28:43
their definitions of allele okay
28:45
so i say dr frelow accepted this
28:47
definition with dr jensen
28:49
after dr jensen corrected him in their
28:51
written debate
28:52
i wonder if dr dan will also admit
28:54
either correction or admit he has been
28:56
applying the correct definition
28:58
erroneously
29:00
how many dna positions in a gene i asked
29:03
how many genes in the genome
29:04
genes obviously consist of more than one
29:06
dna position
29:08
and this is you know the questions i was
29:10
asking speed in our debate
29:12
and i’ve done it in many debates with
29:14
adam heath the zoologist herpetologist
29:16
that was a lot of fun
29:17
because remember they paired a lot of
29:19
the same arguments so
29:21
um so i continue here as dr jensen
29:25
explains in his written debate with dr
29:27
frello by definition genes consist of
29:30
more than one dna position
29:34
so which is it is an allele a version of
29:36
a particular dna position
29:38
or version of a gene that contains
29:39
hundreds to thousands of dna positions
29:42
frello can’t have it both ways stupid
29:45
[ __ ] energy is just killing it with the
29:47
super chats
29:48
don’t worry sw i put the hammer down
29:51
onto whoever blocked you for that time
29:52
being so uh you’re back we like freedom
29:55
of speech here so
29:57
um anybody can comment unless there’s
29:58
trolling going on unless they’re
30:00
spamming
30:01
you know a comment here comment there
30:03
but i’m not i’m gonna you know i’m not
30:05
gonna spend all day in comment sections
30:07
typically i prefer dialogue and debate
30:09
so she says
30:11
you can also have like a faulty dna
30:13
replicase kind of stop over a region of
30:15
dna
30:16
it could fool you into thinking it’s
30:19
lamarcian
30:20
when it’s just stuck over that region
30:23
i gotta say that uh swe i like i like
30:26
her super chats i like her
30:28
input she’s intelligent
30:32
i’ve had debates where the person i was
30:34
debating had no answers to what i was
30:36
bringing up but then
30:37
swe and i got to have a super chat
30:40
debate
30:41
the team skeptic debate comes to mind
30:43
with the chromosome 2 fusion
30:46
okay so let’s see um okay so in my
30:49
refuting the critics book i document
30:51
this interaction between jensen and
30:53
frelo
30:54
which also applies to my interaction
30:55
with dan and you can read this i’m just
30:58
going to go right into what
31:00
jensen says and this is important some
31:03
of this is technical lately
31:05
but it’s the nature of the beast i guess
31:07
when you’re taking on these
31:09
well it to me it seems like dan he felt
31:12
like he had to kind of go
31:13
and almost hide now the arguments in
31:16
like population genetics and
31:18
that which is technical to the point
31:19
where 99.9 of people aren’t going to
31:21
understand the argument
31:23
and i reiterated dan’s argument in the
31:24
comment section to
31:26
some evolutionist named zach and i said
31:27
can you explain this to me what dan
31:29
means
31:30
and he didn’t have an aunt because he
31:31
said i was refuted but then he didn’t
31:32
even know what refuted he did not
31:34
explain the argument so
31:36
like i said you know all they got to do
31:37
is put a response out and they’re going
31:38
to think they won so
31:40
so unfortunately we got to get a little
31:41
technical here but it’s fun it’s fun
31:43
so he says and i see luca in the chat
31:47
so good for luca he he agreed with the
31:49
definition
31:50
he posted the correct definition about
31:52
dna position
31:54
rather than unit okay so let’s see
31:58
the argument rests on his erroneous
32:00
adoption of the second definition
32:02
that alleles are different versions of
32:04
genes under this definition he
32:05
misrepresents my explanation for nuclear
32:08
dna differences
32:09
in fact in one of my published papers
32:12
what’s funny is this paper right here
32:13
the lyle jeans and paper 2016
32:16
was the one that dan said he sourced and
32:19
critiqued
32:20
but yet his misrepresentation
32:24
of the levels of genetic diversity
32:28
in adam and eve the the biblical kinds
32:31
creation when the initial front loading
32:35
event took place was addressed
32:38
in that paper so it’s a lengthy paper i
32:40
doubt he read the whole thing but maybe
32:41
he did maybe he just missed that part so
32:44
and well and even jensen points out that
32:46
he referred to it 15 times in replacing
32:49
darwin so here we go
32:50
frello’s error if an allele is defined
32:53
in terms of a gene
32:54
unit then generating allelic diversity
32:57
diversity by mutating just one gene per
32:59
mutational event
33:00
produces little diversity
33:04
instead if an allele is defined as a
33:06
single genomic position
33:08
okay and what’s nice about luca is he
33:10
provided in the
33:12
um the actual definition um he sourced
33:16
it and this is it this is the correct
33:17
definition
33:18
um so if an allele is defined as a
33:21
single genomic position
33:22
independent of its relationship to a
33:24
gene then enormous
33:26
allelic diversity can be generated by
33:28
mutation
33:29
as an aside allelic diversity need not
33:31
arise via mutation
33:34
again if we use the genomic position
33:36
definition of an allele rather than the
33:37
gene unit definition
33:40
other mechanisms besides mutation can
33:42
generate allelic diversity
33:44
for example a single gene typically
33:47
spans
33:47
thousands of nucleotides so remember
33:50
this is what dan was saying too
33:52
in his hypothetical and snvs right
33:55
single nucleotide variants
33:58
might be distributed throughout that
34:00
gene so for example so jensen’s using
34:02
the
34:03
example of about 90. so let’s say at 90
34:06
of the nucleotides within the gene
34:08
we got snvs okay now if we allow for the
34:11
genomic position definition of alleles
34:15
every single one of these 90 smbs may
34:18
have existed in a heterozygous
34:20
state in each of the individuals of the
34:22
pairs brought on board the earth
34:24
now expanding this single gene example
34:27
across the entire genome reveals a
34:30
tremendous potential
34:31
for allelic diversity on the ark
34:34
in just two diploid individuals
34:37
four genome copies exist since only four
34:41
dna base pairs exist
34:42
virtually every possible genomic
34:45
position allele
34:46
far more than the 4 to 28 gene unit
34:48
alleles could have been present at the
34:50
time of the flood
34:51
if the individuals were heterozygous so
34:54
i read through this yesterday
34:56
i reiterated in the comment section i
34:57
don’t want to bore everybody so read
34:58
through that
35:00
we go here i also did address
35:03
his [ __ ] blood types the hypervariable
35:06
regions
35:07
um yeah so a lengthy
35:11
uh conversation here dan didn’t respond
35:15
of responded in the uh here’s the paper
35:18
again guys please read it
35:20
adam and eve design diversity and allele
35:22
frequencies
35:23
um rj downwards in the chat
35:26
so uh james downer um
35:30
yeah so i’ll i’ll challenge you too
35:32
james the the same challenge i’ve been
35:33
given
35:34
uh erica dan take the abiogenesis
35:38
challenge and
35:38
i want you i challenge you to go through
35:40
this paper here
35:42
um adam and eve design diversity and
35:45
allele frequencies
35:46
refute it you won’t be able to and
35:50
also go through the hat map data go
35:52
through the lecture i provided in in the
35:53
last video
35:54
everything dan dodged team dodgeball
35:59
dodge duck dip dive and dodge five d’s
36:02
of dodgeball so yeah
36:03
we’ll be looking forward to that that
36:06
video there rj
36:07
i doubt we’ll get it though okay so
36:10
let’s go to dan’s argument now he had he
36:14
had no dispute to the definition
36:16
maybe he’s going to be like frello and
36:17
actually adopt the accurate definition.

4 posts were split to a new topic: Carter: Were Recombination Rates Higher in the Past?