On Feb 27, 2024, Hemidactylus* wrote
(in article<2XKdnS5_L_KKD0P4nZ2dnZfqnPqdnZ2d@giganews.com>):

> John Harshman<john.harshman@gmail.com> wrote:
> > On 2/27/24 5:06 AM, Ernest Major wrote:
> > > On 27/02/2024 12:29, jillery wrote:
> > > > On Tue, 20 Feb 2024 08:24:20 -0800 (PST), Burkhard
> > > > <b.schafer@ed.ac.uk> wrote:
> > > >
> > > > > I just saw this:
> > > > > https://www.templeshalloranfuneralhome.com/obituary/dr-peter-nyikos
> > > > >
> > > > > assuming it's genuine (and I have no reason to doubt this) , the
> > > > > details fit, as does his extended absence from posting. He could be a
> > > > > royal pain in the backside, but I do hope he now experiences the type
> > > > > of heaven he always hoped for (with a <10% certainty, of course>
> > > > > That the GG version of TO will survive him by barely a week, before
> > > > > getting archived forever, is maybe the most fitting memorial imaginable.
> > > >
> > > >
> > > > For anybody who might care about such things, the above post is one of
> > > > a dozen which Eternal September failed to capture.
> > >
> > > It did have it originally, but has since disappeared ("expired"). The
> > > same happened to a couple of posts from MarkE.
> >
> > Well, you have to admit that "expired" is appropriate in this case.
> Still too soon.

Oh, Petey the Grate hit his sell-by date at least 20 years ago.

On Feb 27, 2024, RonO wrote
(in article <urltam$3fj4a$1@dont-email.me>):

> On 2/20/2024 11:13 AM, Ernest Major wrote:
> > On 20/02/2024 17:05, Martin Harran wrote:
> > > On Tue, 20 Feb 2024 16:49:20 +0000, Martin Harran
> > > <martinharran@gmail.com> wrote:
> > >
> > > > .... I thought it might not be him as it seems strange that he would
> > > > still
> > > > be employed as a lecturer at 80 years of age.
> > >
> > > Brain fart - 78 years of age.
> >
> > 77; he would have been 78 next month.
>
> For some reason my posts are not showing up. I've had trouble just
> getting eternal september to open posts. I was updated, and had to
> reload TO, but nothing has been working. I posted to the Dirt DNA
> thread, but it didn't show up. For the last couple of weeks when I
> click on a post it either opens to a blank page or it goes to a bar at
> the top of the window and ony a partial post is displayed below. It is
> a worthless feature that should have never been implemented. Why would
> anyone want to accumulate partial posts in a bar across the top of the
> window? Once in a while I can open a post and even respond to it like I
> did with the Dirt DNA thread, but it doesn't seem to work.

you seem to be using Thunderbird. Thunderbird is a mail client which can be
used to read usenet. Thunderbird has... issues. I would try a dedicated
newsreader if I were you.
>
>
> So this is sort of a test post.
>
> Nyikos had to prevaricate and lie about the Phillip Johnson quote where
> Johnson admitted that the ID science didn't exist and that he had given
> up on teaching ID in the public schools after the Dover decision.
> Nyikos would usually just snip and run from the quote, but once he put
> up the lame argument that Johnson could be disregarded because he was
> old. Nyikos, at that time, was older than Phillip Johnson when Johnson
> had made the quote (Johnson had been 65 years old). So Nyikos claimed
> that he was old enough so that his opinions could be disregarded. A
> true TO tale.
>
> Ron Okimoto

On Wed, 28 Feb 2024 07:19:01 -0500, WolfFan <akwolffan@zoho.com>
wrote:

>On Feb 27, 2024, Hemidactylus* wrote
>(in article<2XKdnS5_L_KKD0P4nZ2dnZfqnPqdnZ2d@giganews.com>):
>
>> John Harshman<john.harshman@gmail.com> wrote:
>> > On 2/27/24 5:06 AM, Ernest Major wrote:
>> > > On 27/02/2024 12:29, jillery wrote:
>> > > > On Tue, 20 Feb 2024 08:24:20 -0800 (PST), Burkhard
>> > > > <b.schafer@ed.ac.uk> wrote:
>> > > >
>> > > > > I just saw this:
>> > > > > https://www.templeshalloranfuneralhome.com/obituary/dr-peter-nyikos
>> > > > >
>> > > > > assuming it's genuine (and I have no reason to doubt this) , the
>> > > > > details fit, as does his extended absence from posting. He could be a
>> > > > > royal pain in the backside, but I do hope he now experiences the type
>> > > > > of heaven he always hoped for (with a <10% certainty, of course>
>> > > > > That the GG version of TO will survive him by barely a week, before
>> > > > > getting archived forever, is maybe the most fitting memorial imaginable.
>> > > >
>> > > >
>> > > > For anybody who might care about such things, the above post is one of
>> > > > a dozen which Eternal September failed to capture.
>> > >
>> > > It did have it originally, but has since disappeared ("expired"). The
>> > > same happened to a couple of posts from MarkE.
>> >
>> > Well, you have to admit that "expired" is appropriate in this case.
>> Still too soon.
>
>Oh, Petey the Grate hit his sell-by date at least 20 years ago.

True, but his ghost continues to haunt T.O.'s hallowed halls even
beyond the grave.

--
To know less than we don't know is the nature of most knowledge

On 2/28/24 12:31 AM, J. J. Lodder wrote:
> *Hemidactylus* <ecphoric@allspamis.invalid> wrote:
>
>> Burkhard <b.schafer@ed.ac.uk> wrote:
>>> I just saw this:
>>> https://www.templeshalloranfuneralhome.com/obituary/dr-peter-nyikos
>>>
>>> assuming it's genuine (and I have no reason to doubt this) , the details
>>> fit, as does his extended absence from posting. He could be a royal pain
>>> in the backside, but I do hope he now experiences the type of heaven he
>>> always hoped for (with a <10% certainty, of course> That the GG version
>>> of TO will survive him by barely a week, before getting archived
>>> forever, is maybe the most fitting memorial imaginable.
>>>
>> The birthdate in the death notice matches his CV:
>> https://sc.edu/study/colleges_schools/artsandsciences/mathematics/our_people/p
> rofile_cv/nyikos_peter_cv.pdf
>
> No surprise here:
> He was the kind of mathematician I would have expected.
>
> Jan
>
It's a pretty obscure corner of math. A mathematician friend many years
ago told me that if I ever find myself having doubts about the validity
of arithmetic, I should consult either a psychiatrist or a point-set
topologist. He further suggested that going to the psychiatrist first
would just save time.

On 2/28/24 4:25 AM, WolfFan wrote:
> On Feb 27, 2024, RonO wrote
> (in article <urltam$3fj4a$1@dont-email.me>):
>
>> On 2/20/2024 11:13 AM, Ernest Major wrote:
>>> On 20/02/2024 17:05, Martin Harran wrote:
>>>> On Tue, 20 Feb 2024 16:49:20 +0000, Martin Harran
>>>> <martinharran@gmail.com> wrote:
>>>>
>>>>> .... I thought it might not be him as it seems strange that he would
>>>>> still
>>>>> be employed as a lecturer at 80 years of age.
>>>>
>>>> Brain fart - 78 years of age.
>>>
>>> 77; he would have been 78 next month.
>>
>> For some reason my posts are not showing up. I've had trouble just
>> getting eternal september to open posts. I was updated, and had to
>> reload TO, but nothing has been working. I posted to the Dirt DNA
>> thread, but it didn't show up. For the last couple of weeks when I
>> click on a post it either opens to a blank page or it goes to a bar at
>> the top of the window and ony a partial post is displayed below. It is
>> a worthless feature that should have never been implemented. Why would
>> anyone want to accumulate partial posts in a bar across the top of the
>> window? Once in a while I can open a post and even respond to it like I
>> did with the Dirt DNA thread, but it doesn't seem to work.
>
> you seem to be using Thunderbird. Thunderbird is a mail client which can be
> used to read usenet. Thunderbird has... issues. I would try a dedicated
> newsreader if I were you.
>>
>>
>> So this is sort of a test post.
>>
>> Nyikos had to prevaricate and lie about the Phillip Johnson quote where
>> Johnson admitted that the ID science didn't exist and that he had given
>> up on teaching ID in the public schools after the Dover decision.
>> Nyikos would usually just snip and run from the quote, but once he put
>> up the lame argument that Johnson could be disregarded because he was
>> old. Nyikos, at that time, was older than Phillip Johnson when Johnson
>> had made the quote (Johnson had been 65 years old). So Nyikos claimed
>> that he was old enough so that his opinions could be disregarded. A
>> true TO tale.
>>
>> Ron Okimoto
>
>
Any software has some issues, Thunderbird included. It does what it
does, but it does fine for me. I've been using it for reading email for
many years.

erik simpson <eastside.erik@gmail.com> wrote:
> On 2/28/24 4:25 AM, WolfFan wrote:
>> On Feb 27, 2024, RonO wrote
>> (in article <urltam$3fj4a$1@dont-email.me>):
>>
>>> On 2/20/2024 11:13 AM, Ernest Major wrote:
>>>> On 20/02/2024 17:05, Martin Harran wrote:
>>>>> On Tue, 20 Feb 2024 16:49:20 +0000, Martin Harran
>>>>> <martinharran@gmail.com> wrote:
>>>>>
>>>>>> .... I thought it might not be him as it seems strange that he would
>>>>>> still
>>>>>> be employed as a lecturer at 80 years of age.
>>>>>
>>>>> Brain fart - 78 years of age.
>>>>
>>>> 77; he would have been 78 next month.
>>>
>>> For some reason my posts are not showing up. I've had trouble just
>>> getting eternal september to open posts. I was updated, and had to
>>> reload TO, but nothing has been working. I posted to the Dirt DNA
>>> thread, but it didn't show up. For the last couple of weeks when I
>>> click on a post it either opens to a blank page or it goes to a bar at
>>> the top of the window and ony a partial post is displayed below. It is
>>> a worthless feature that should have never been implemented. Why would
>>> anyone want to accumulate partial posts in a bar across the top of the
>>> window? Once in a while I can open a post and even respond to it like I
>>> did with the Dirt DNA thread, but it doesn't seem to work.
>>
>> you seem to be using Thunderbird. Thunderbird is a mail client which can be
>> used to read usenet. Thunderbird has... issues. I would try a dedicated
>> newsreader if I were you.
>>>
>>>
>>> So this is sort of a test post.
>>>
>>> Nyikos had to prevaricate and lie about the Phillip Johnson quote where
>>> Johnson admitted that the ID science didn't exist and that he had given
>>> up on teaching ID in the public schools after the Dover decision.
>>> Nyikos would usually just snip and run from the quote, but once he put
>>> up the lame argument that Johnson could be disregarded because he was
>>> old. Nyikos, at that time, was older than Phillip Johnson when Johnson
>>> had made the quote (Johnson had been 65 years old). So Nyikos claimed
>>> that he was old enough so that his opinions could be disregarded. A
>>> true TO tale.
>>>
>>> Ron Okimoto
>>
>>
> Any software has some issues, Thunderbird included. It does what it
> does, but it does fine for me. I've been using it for reading email for
> many years.
>
T-bird worked fine for me. I kinda liked Pan too. KNode was my fave but was
linked to the KDE monstrosity, which I mostly didn’t like.

erik simpson <eastside.erik@gmail.com> wrote:

> On 2/28/24 12:31 AM, J. J. Lodder wrote:
> > *Hemidactylus* <ecphoric@allspamis.invalid> wrote:
> >
> >> Burkhard <b.schafer@ed.ac.uk> wrote:
> >>> I just saw this:
> >>> https://www.templeshalloranfuneralhome.com/obituary/dr-peter-nyikos
> >>>
> >>> assuming it's genuine (and I have no reason to doubt this) , the details
> >>> fit, as does his extended absence from posting. He could be a royal pain
> >>> in the backside, but I do hope he now experiences the type of heaven he
> >>> always hoped for (with a <10% certainty, of course> That the GG version
> >>> of TO will survive him by barely a week, before getting archived
> >>> forever, is maybe the most fitting memorial imaginable.
> >>>
> >> The birthdate in the death notice matches his CV:
> >> https://sc.edu/study/colleges_schools/artsandsciences/mathematics/our_peopl
e/p
> > rofile_cv/nyikos_peter_cv.pdf
> >
> > No surprise here:
> > He was the kind of mathematician I would have expected.
> >
> > Jan
> >
> It's a pretty obscure corner of math.

Yes, completely divorced from any connection with reality.
I had some discussions with him about fine-tuning,
and found him to be clueless about the physics of it.
That said, he was willing and capable to learn.
(and to forget again)

> A mathematician friend many years
> ago told me that if I ever find myself having doubts about the validity
> of arithmetic, I should consult either a psychiatrist or a point-set
> topologist. He further suggested that going to the psychiatrist first
> would just save time.

I think I agree. If faced with it many years ago
I would have consulted Imre Lakatos,
and I would have asked him if all this is a typical example
of 'a degenerating research program' within mathematics.
By Lakatos' definition a degenerating research program
doesn't deal with real problems,
but only with problems generated by the program itself.
That said, Peter was probaby good at it.

A real mathematician, like Erdos for example,
would look down upon it with contempt, I guess,
as 'much ado about nothing',
and not contributing to pushing back the SF.

Jan
(but what do I know)

--
"Ich glaube das er ein Hochstapler ist."
"Beweisen kan ich es aber nicht."
"Dazu sollte ich seine Werke lesen, und das fallt mich schwer."
(Wolfgang Pauli)

On Tue, 27 Feb 2024 18:04:38 -0600, RonO <rokimoto@cox.net> wrote:

>I posted to the Dirt DNA thread, but it didn't show up.

If you still have a copy of what you posted, I would be very
interested to read it. Repost?

--
To know less than we don't know is the nature of most knowledge

On 2/28/2024 9:53 PM, jillery wrote:
> On Tue, 27 Feb 2024 18:04:38 -0600, RonO <rokimoto@cox.net> wrote:
>
>> I posted to the Dirt DNA thread, but it didn't show up.
>
>
> If you still have a copy of what you posted, I would be very
> interested to read it. Repost?
>
> --
> To know less than we don't know is the nature of most knowledge
>

It was about the limitations of the technology. The paper that you put
up was using PCR to amplify the DNA before sequencing. You can only
amplify short pieces because the DNA is degraded, and you need to either
know the sequence of what you are amplifying or you have to try to find
some highly conserved sequences in which to amplify, but Highly
conserved sequence, is highly conserved and you will only be able to
identify species that are distantly enough related to have a different
sequence that can be identified using that primer set. You also have to
deal with the degraded DNA sequence and things like the deamination of
cytosines over time.

Success will be limited to how long the surviving DNA fragments are in
the soil samples.

We have tech that will sequence short fragments without PCR
amplification, but at this time the sequence error rates are high 10 to
20% can be erroneous calls for nanopore sequencing, so they aren't much
good at identifying specific short fragments to specific species. What
we need to develop to make biome sequencing really useful is a highly
accurate means of sequencing the short fragments that survive in the
soil samples. It might be possible with current short read technology,
but they haven't been trying it. You need to ligate sequence tags to
the ends of the fragments (PCR can be used to do a little amplification)
and then sequence the mess, but that isn't what they are doing.

This may be due to the fact that most of the DNA that they find in these
types of samples is from bacteria and fungi.

Ron Okimoto

On Sun, 3 Mar 2024 14:11:14 -0600, RonO <rokimoto@cox.net> wrote:

>On 2/28/2024 9:53 PM, jillery wrote:
>> On Tue, 27 Feb 2024 18:04:38 -0600, RonO <rokimoto@cox.net> wrote:
>>
>>> I posted to the Dirt DNA thread, but it didn't show up.
>>
>>
>> If you still have a copy of what you posted, I would be very
>> interested to read it. Repost?
>>
>>
>
>It was about the limitations of the technology. The paper that you put
>up was using PCR to amplify the DNA before sequencing. You can only
>amplify short pieces because the DNA is degraded, and you need to either
>know the sequence of what you are amplifying or you have to try to find
>some highly conserved sequences in which to amplify, but Highly
>conserved sequence, is highly conserved and you will only be able to
>identify species that are distantly enough related to have a different
>sequence that can be identified using that primer set. You also have to
>deal with the degraded DNA sequence and things like the deamination of
>cytosines over time.
>
>Success will be limited to how long the surviving DNA fragments are in
>the soil samples.
>
>We have tech that will sequence short fragments without PCR
>amplification, but at this time the sequence error rates are high 10 to
>20% can be erroneous calls for nanopore sequencing, so they aren't much
>good at identifying specific short fragments to specific species. What
>we need to develop to make biome sequencing really useful is a highly
>accurate means of sequencing the short fragments that survive in the
>soil samples. It might be possible with current short read technology,
>but they haven't been trying it. You need to ligate sequence tags to
>the ends of the fragments (PCR can be used to do a little amplification)
>and then sequence the mess, but that isn't what they are doing.
>
>This may be due to the fact that most of the DNA that they find in these
>types of samples is from bacteria and fungi.
>
>Ron Okimoto

IIUC you're saying the paper's claims are false, that their evidence
doesn't support the claim of identifying biomes full ancient species
from DNA collected from dirt.

--
To know less than we don't know is the nature of most knowledge

On 3/5/24 10:07 PM, jillery wrote:
> On Sun, 3 Mar 2024 14:11:14 -0600, RonO <rokimoto@cox.net> wrote:
>
>> On 2/28/2024 9:53 PM, jillery wrote:
>>> On Tue, 27 Feb 2024 18:04:38 -0600, RonO <rokimoto@cox.net> wrote:
>>>
>>>> I posted to the Dirt DNA thread, but it didn't show up.
>>>
>>>
>>> If you still have a copy of what you posted, I would be very
>>> interested to read it. Repost?
>>>
>>>
>>
>> It was about the limitations of the technology. The paper that you put
>> up was using PCR to amplify the DNA before sequencing. You can only
>> amplify short pieces because the DNA is degraded, and you need to either
>> know the sequence of what you are amplifying or you have to try to find
>> some highly conserved sequences in which to amplify, but Highly
>> conserved sequence, is highly conserved and you will only be able to
>> identify species that are distantly enough related to have a different
>> sequence that can be identified using that primer set. You also have to
>> deal with the degraded DNA sequence and things like the deamination of
>> cytosines over time.
>>
>> Success will be limited to how long the surviving DNA fragments are in
>> the soil samples.
>>
>> We have tech that will sequence short fragments without PCR
>> amplification, but at this time the sequence error rates are high 10 to
>> 20% can be erroneous calls for nanopore sequencing, so they aren't much
>> good at identifying specific short fragments to specific species. What
>> we need to develop to make biome sequencing really useful is a highly
>> accurate means of sequencing the short fragments that survive in the
>> soil samples. It might be possible with current short read technology,
>> but they haven't been trying it. You need to ligate sequence tags to
>> the ends of the fragments (PCR can be used to do a little amplification)
>> and then sequence the mess, but that isn't what they are doing.
>>
>> This may be due to the fact that most of the DNA that they find in these
>> types of samples is from bacteria and fungi.
>>
>> Ron Okimoto
>
>
> IIUC you're saying the paper's claims are false, that their evidence
> doesn't support the claim of identifying biomes full ancient species
> from DNA collected from dirt.
>
> --
> To know less than we don't know is the nature of most knowledge
>
I wondered about that too. I watched the show, and noticed that the
identifications of DNA contributors were things that were already known
to be present. Now if something were identified that was a surprise,
that would be another story.

On Wed, 6 Mar 2024 08:09:30 -0800, erik simpson
<eastside.erik@gmail.com> wrote:

>On 3/5/24 10:07 PM, jillery wrote:
>> On Sun, 3 Mar 2024 14:11:14 -0600, RonO <rokimoto@cox.net> wrote:
>>
>>> On 2/28/2024 9:53 PM, jillery wrote:
>>>> On Tue, 27 Feb 2024 18:04:38 -0600, RonO <rokimoto@cox.net> wrote:
>>>>
>>>>> I posted to the Dirt DNA thread, but it didn't show up.
>>>>
>>>>
>>>> If you still have a copy of what you posted, I would be very
>>>> interested to read it. Repost?
>>>>
>>>>
>>>
>>> It was about the limitations of the technology. The paper that you put
>>> up was using PCR to amplify the DNA before sequencing. You can only
>>> amplify short pieces because the DNA is degraded, and you need to either
>>> know the sequence of what you are amplifying or you have to try to find
>>> some highly conserved sequences in which to amplify, but Highly
>>> conserved sequence, is highly conserved and you will only be able to
>>> identify species that are distantly enough related to have a different
>>> sequence that can be identified using that primer set. You also have to
>>> deal with the degraded DNA sequence and things like the deamination of
>>> cytosines over time.
>>>
>>> Success will be limited to how long the surviving DNA fragments are in
>>> the soil samples.
>>>
>>> We have tech that will sequence short fragments without PCR
>>> amplification, but at this time the sequence error rates are high 10 to
>>> 20% can be erroneous calls for nanopore sequencing, so they aren't much
>>> good at identifying specific short fragments to specific species. What
>>> we need to develop to make biome sequencing really useful is a highly
>>> accurate means of sequencing the short fragments that survive in the
>>> soil samples. It might be possible with current short read technology,
>>> but they haven't been trying it. You need to ligate sequence tags to
>>> the ends of the fragments (PCR can be used to do a little amplification)
>>> and then sequence the mess, but that isn't what they are doing.
>>>
>>> This may be due to the fact that most of the DNA that they find in these
>>> types of samples is from bacteria and fungi.
>>>
>>> Ron Okimoto
>>
>>
>> IIUC you're saying the paper's claims are false, that their evidence
>> doesn't support the claim of identifying biomes full ancient species
>> from DNA collected from dirt.
>>
>>
>I wondered about that too. I watched the show, and noticed that the
>identifications of DNA contributors were things that were already known
>to be present. Now if something were identified that was a surprise,
>that would be another story.

Here are the three links I provided in the OP:

<https://www.pbs.org/video/hunt-for-the-oldest-dna-zckys0/>
<https://www.youtube.com/watch?v=c2ppreiB1PQ>
<https://www.sciencedirect.com/science/article/pii/S0006320714004443>

The video provides a description of the history of Eske Willerslev's
efforts to extract what he calls environmental DNA, where he says he's
able to isolate and identify the species of plants and animals using
DNA from soil samples. These are remarkable claims.

It's reasonable in the beginning that he compared his DNA extractions
to known genomes, in order to confirm that his methods in fact provide
identifiable DNA sequences. He discusses this @35:30. I believe this
is the part of the video to which you allude above.

ISTM it's remarkable enough that his methods reliably assemble
identifiable DNA from dirt. On top of that, @42:02 he describes
identifying mastodon DNA in Greenland, which was previously unknown to
have existed there. On top of that, he claims to be able to identify
entire ecosystems from over 2mya. These claims go far beyond what I
understand is your understanding of his claims.

--
To know less than we don't know is the nature of most knowledge

On 3/6/2024 12:07 AM, jillery wrote:
> On Sun, 3 Mar 2024 14:11:14 -0600, RonO <rokimoto@cox.net> wrote:
>
>> On 2/28/2024 9:53 PM, jillery wrote:
>>> On Tue, 27 Feb 2024 18:04:38 -0600, RonO <rokimoto@cox.net> wrote:
>>>
>>>> I posted to the Dirt DNA thread, but it didn't show up.
>>>
>>>
>>> If you still have a copy of what you posted, I would be very
>>> interested to read it. Repost?
>>>
>>>
>>
>> It was about the limitations of the technology. The paper that you put
>> up was using PCR to amplify the DNA before sequencing. You can only
>> amplify short pieces because the DNA is degraded, and you need to either
>> know the sequence of what you are amplifying or you have to try to find
>> some highly conserved sequences in which to amplify, but Highly
>> conserved sequence, is highly conserved and you will only be able to
>> identify species that are distantly enough related to have a different
>> sequence that can be identified using that primer set. You also have to
>> deal with the degraded DNA sequence and things like the deamination of
>> cytosines over time.
>>
>> Success will be limited to how long the surviving DNA fragments are in
>> the soil samples.
>>
>> We have tech that will sequence short fragments without PCR
>> amplification, but at this time the sequence error rates are high 10 to
>> 20% can be erroneous calls for nanopore sequencing, so they aren't much
>> good at identifying specific short fragments to specific species. What
>> we need to develop to make biome sequencing really useful is a highly
>> accurate means of sequencing the short fragments that survive in the
>> soil samples. It might be possible with current short read technology,
>> but they haven't been trying it. You need to ligate sequence tags to
>> the ends of the fragments (PCR can be used to do a little amplification)
>> and then sequence the mess, but that isn't what they are doing.
>>
>> This may be due to the fact that most of the DNA that they find in these
>> types of samples is from bacteria and fungi.
>>
>> Ron Okimoto
>
>
> IIUC you're saying the paper's claims are false, that their evidence
> doesn't support the claim of identifying biomes full ancient species
> from DNA collected from dirt.

I did not say that their claims were false. I just stated the
limitations of what they were doing, and there is a bias in what they
find. Essentially, they find things that they can look for and
differentiate from each other, not necessarily everything that was there.

Ron Okimoto
>
> --
> To know less than we don't know is the nature of most knowledge
>

On Fri, 8 Mar 2024 17:18:33 -0600, RonO <rokimoto@cox.net> wrote:

>On 3/6/2024 12:07 AM, jillery wrote:
>> On Sun, 3 Mar 2024 14:11:14 -0600, RonO <rokimoto@cox.net> wrote:
>>
>>> On 2/28/2024 9:53 PM, jillery wrote:
>>>> On Tue, 27 Feb 2024 18:04:38 -0600, RonO <rokimoto@cox.net> wrote:
>>>>
>>>>> I posted to the Dirt DNA thread, but it didn't show up.
>>>>
>>>>
>>>> If you still have a copy of what you posted, I would be very
>>>> interested to read it. Repost?
>>>>
>>>>
>>>
>>> It was about the limitations of the technology. The paper that you put
>>> up was using PCR to amplify the DNA before sequencing. You can only
>>> amplify short pieces because the DNA is degraded, and you need to either
>>> know the sequence of what you are amplifying or you have to try to find
>>> some highly conserved sequences in which to amplify, but Highly
>>> conserved sequence, is highly conserved and you will only be able to
>>> identify species that are distantly enough related to have a different
>>> sequence that can be identified using that primer set. You also have to
>>> deal with the degraded DNA sequence and things like the deamination of
>>> cytosines over time.
>>>
>>> Success will be limited to how long the surviving DNA fragments are in
>>> the soil samples.
>>>
>>> We have tech that will sequence short fragments without PCR
>>> amplification, but at this time the sequence error rates are high 10 to
>>> 20% can be erroneous calls for nanopore sequencing, so they aren't much
>>> good at identifying specific short fragments to specific species. What
>>> we need to develop to make biome sequencing really useful is a highly
>>> accurate means of sequencing the short fragments that survive in the
>>> soil samples. It might be possible with current short read technology,
>>> but they haven't been trying it. You need to ligate sequence tags to
>>> the ends of the fragments (PCR can be used to do a little amplification)
>>> and then sequence the mess, but that isn't what they are doing.
>>>
>>> This may be due to the fact that most of the DNA that they find in these
>>> types of samples is from bacteria and fungi.
>>>
>>> Ron Okimoto
>>
>>
>> IIUC you're saying the paper's claims are false, that their evidence
>> doesn't support the claim of identifying biomes full ancient species
>> from DNA collected from dirt.
>
>I did not say that their claims were false. I just stated the
>limitations of what they were doing, and there is a bias in what they
>find. Essentially, they find things that they can look for and
>differentiate from each other, not necessarily everything that was there.

You're technically correct. You didn't write the specific words
"their claims are false". I should have been more explicit that the
limitations to which you refer are contrary to their claims. Silly
me.

Also, they didn't claim they could find "everything that was there".
They do claim they could identify numerous plant and animal species
which broadly describe biomes.

--
To know less than we don't know is the nature of most knowledge