Vahid Majidi is the head of the FBI’s WMD unit. He has put forward the theory of indel identification based on the work of himself and his team including outside scientists. Jacques Ravel is one of the scientists who has worked on this.
However, there are assumptions and pitfalls in this claim that may result in the whole thing being junk science, i.e. they can’t identify RMR1029 the flask at Ft. Detrick of Bruce Ivins as the source to the exclusion of the other 1000 flasks tested or some subset larger than 8.
In 1981, Ames strain was isolated from a single cow. That cow likely ingested anthrax spores from the soil or water, became sick and died. Some of the anthrax was then sent on in the form of a blood sample or ear. The lethal dose in humans for inhalation anthrax is often stated as 10,000 spores. For a cow to ingest it, the dose didn’t show up in internet searches. Cattle farmers and human volunteers for determining the exact lethal dose in cows and humans seem to be scarce.
The FBI claims to have asked 1000 labs to send samples. From these they grew anthrax colonies and allegedly identified which colonies showed different appearance, morphs, and then from that identified indels, changes in the DNA molecule. Whether that really is true is something the FBI needs to prove.
If they grew 1000 colonies from each lab, that is the same as testing 1000 spores for the indels. Within a spore how many DNA molecules are being tested? We can assume its one for now, but it is really more. This introduces an additional complication, which we ignore for now.
The FBI claim is that the original Ames strain had one morph despite the cow having ingested more than one spore to get sick and die. The cow might have ingested a microgram of anthrax spores. 1 gram has 1 trillion spores, so a microgram has 1 billion spores. If the cow ingested 1 billion spores, and the FBI tested 1000 labs x 1000 colonies (= spores) each then the FBI tested 1 million spores total v. the 1 billion spores the cow ingested in that scenario.
The FBI claims that 8 morphs evolved from 1981 to 2001 from the Ames Strain and that it tested for 4 and that the original Ames spore sample had one single indel type in it.
Alternative Hypothesis: All 8 morphs the FBI has found of indels were present in the 1981 sample of spores that killed the cow and were eventually transmitted to the US research community.
Under the FBI hypothesis, 8 indels evolved in 20 years with a small amount of anthrax in labs. But shouldn’t nature over millions of years have evolved a lot more? If 8 indels are produced every 20 years in the labs with a few small runs, then shouldn’t nature have produced a staggering number of indels in wild anthrax? This can be tested by testing wild Ames anthrax for how many indels there are, and whether they include the 8 the FBI has found in lab anthrax from the single Ames source.
Is it really true that no more wild anthrax was added to the lab stocks and thus added wild indels grown over the last million years on the entire planet earth?
One comparison to keep in mind is the 1 million spores tested by the FBI total, or perhaps 100 thousand to 10 million tested to what the cow ingested, which could have easily been 1 billion spores.
What anthrax colonies look like:
http://www3.niaid.nih.gov/NR/rdonlyres/DD661CCD-4E1E-4918-832B-DA66873C6037/0/ANDB3E_1.JPG
To test 1000 labs, they grew 1000 colonies each for a total of 1 million colonies? Then they looked at them to identify the strange ones? If one looks at above photo of anthrax this seems preposterous. One person did the looking or many people? At the source labs or at a central lab? Someone at a central lab looked at 1 million colonies? How long did that take? Aren’t these differences in colony appearances subjective? Don’t colonies grow randomly? Isn’t that how the colony photos on the Internet look?
==
If they claim they do a million colonies per lab flask source, then how do they inspect them? 1 second each is 1 million seconds per lab flask. 3600 seconds in an hour, so about 300 hours per lab flask.
If they claim they can look at them all at once and see the morphs, then is that believable given the photo above? If one has a million they aren’t all flat one colony layer thick. So you can miss them behind them.
Once still gets statistics issues if one of the indels has a low probability frequency.
There is also the issue of how much variation there is in colony appearance from other factors. Are they fooling themselves on the link from indel to morph appearance? Isn’t there additional random variation? Is the causal relation tested? As a statistical relation? Have they formulated classifications of the variation of visual appearance for the same indel? Can they use statistics for that? How do they do statistics if all identification is visual, just looking at a million colonies at a time?
How do they manage all this without errors creeping in? How do the get it into numbers on computer hard drives to keep track of? What data is on computer hard drives? What isn’t?
Can they simulate the entire process from the cow in 1981 to present including the testing and the statistical variation in everything?
Rough Notes:
http://www.ph.ucla.edu/epi/bioter/theamesstrain.html
lethal dose of anthrax is 10000 spores?
“
A lethal infection is reported to result from inhalation of about 10,000–20,000 spores, though this dose varies amongst host species.[13]
“
lethal dose in stomach of cow is more than inhalation anthrax
in humans?
and it can eat more than the minimum lethal dose.
so it ate 1 million spores?
and those had more indel morphs than testing
10000 colonies from a lab.
http://www3.niaid.nih.gov/NR/rdonlyres/DD661CCD-4E1E-4918-832B-DA66873C6037/0/ANDB3E_1.JPG
1000 labs have lab assistants from anywhere in the world.
who don’t care.
http://www.ph.ucla.edu/epi/bioter/theamesstrain.html
cow ingested at least 10,000 but more likely 1 million
to 1 billion spores.
http://www.vetmed.ucdavis.edu/vetext/INF-BE_cca/INF-BE_cca01/INF-BE_cca0112.html
http://www.cattletoday.com/archive/2001/November/CT177.shtml
== More rough notes
equation author:J author:Ravel
author:v-majidi
==
compartmentalization and lack of understanding what doing.
==
If they grow 1000 colonies from a lab flask, that is more work to identify the morph ones. There must be random variation in the appearance. Different people are doing this work.
From NYT
“Then an Army microbiologist from Fort Detrick made an unexpected discovery. Using an old-fashioned microbiological technique, he spread out some attack spores on a bed of nutrient and let each form its own colony. All the colonies looked identical except one, which, to his trained eye, seemed very slightly different. Different-looking colonies are called morphotypes or just “morphs.”
“Had that task been assigned to someone less experienced, these morphotypes might never have been seen or their significance never realized,” Dr. Fraser-Liggett said.”
So out of the 1000 labs tested, some had untrained eyes looking at the colonies grown. If each lab grew over 1000 colonies that is a problem for untrained eyes. Also compartmentalization made it harder to achieve consistency. People would need to be trained what to look for.
So if they grow 1000′s of colonies per lab flask, then untrained eyes will glaze over to miss the perhaps single morph colony to be found. If they grow under 100 colonies they miss growing the morph colonies because the article says they are under 1 percent each.
==Some posts at Meryl Nass on this
https://www.blogger.com/comment.g?blogID=6592607595936297457&postID=4547196115304895388&isPopup=true
http://anthraxvaccine.blogspot.com/2008/12/new-details-from-genomic-forensic.html
To avoid confusion, the FBI or someone has to give names to each morph and list in a table which ones were in which letters.
Its possible that there is also not a unified definition of what 4 variants means in the project. Some people think it means some sort of original plus 4 additional and others think that 4 means the 4 named morphs that are distinct from the original.
They should also have a photo of each colony and its name and explain why they think they look different from other morphs and what the variation of appearance is when the same morph is present.
Also, what are the percentages of each morph in the original flask and in the other 7 flasks (or is it 8?) that have it. Give the name of each lab that has the same batch as at Detrick.
Also what about other morphs they decided not to pursue? Science is supposed to falsify hypotheses not just convict dead men. How about a second team tries to break the first one’s results by finding other morphs not in the Ft. Detrick flask but in someone else’s?
- Old Atlantic Lighthouse said…
- What about a single morph in one letter that is only in one lab flask? Or is in a lab flask different than RMR1029 and not in RMR1029? Those cases should be pursued next. Basically, any morph in any letter is back tested against all the flasks. Publish the entire table.
- Old Atlantic Lighthouse said…
- The FBI’s thinking is: We know in advance the letter anthrax all came from a single flask, that of the lone nut. They decided that in advance, and their methodology builds that in. However, if one drops that assumption, there are other possibilities. Two or more sources sent independently. Two or more with mixing after powder is produced, possibly because not enough, and so on.
- Old Atlantic Lighthouse said…
- “he spread out some attack spores on a bed of nutrient and let each form its own colony. All the colonies looked identical except one, which, to his trained eye, seemed very slightly different. Different-looking colonies are called morphotypes or just “morphs.””
You can’t tell until you grow them if they are different. So the anthrax in the letters can contain any number of morphs. Unless you grow all the anthrax in a letter you can’t know if you got all the morphs in the letter. So we have to have a stopping rule. One stopping rule is do all. But they probably kept some.
“Dr. Ravel was asked to decode seven more morph genomes,”
So 8 morphs total.
But there could be more.
The entire procedure had a stopping rule of convicting a lone wolf scientist. Stop growing and testing and comparing when you do that. But that is not trying to disprove your hypothesis.
- Old Atlantic Lighthouse said…
- Maybe the 8 labs that found all 4 morphs were the 8 labs that grew 1000 or more colonies? The other labs grew fewer colonies? Monte Carlo was used at Los Alamos early on. Vahid Majidi is from Los Alamos.
We need a table of how many colonies grown by each lab and which morphs they found. We also need to know how many times they went back to grow more colonies from the Ivins flask until they got all 4 from that flask they were looking for, and whether they decided which of the 8 to look for after they concluded 4 were not in the Ivins flask.
- Old Atlantic Lighthouse said…
- “Though 99 percent of its spores were identical with the Ames ancestor, some 1 percent or less were morphs. “
” As the morphs became available, the F.B.I. started testing samples. At first, some had one or two of the morphs. None had three of the morphs.
By late 2005 to 2006 it became clear that just eight of the 1,070 samples collected included all four morphs.”
Because they started growing more colonies when they didn’t find all 4?
Let p[i][j] be the percentage of morph i in flask j. This is not a constant of nature. A flask can have a low percentage but still be there. If one grows 1000 colonies and p[i][j] is .01 in one flask and
.0001 in another, then you may not get it when testing that flask.
If a person was the bad guy he could just grow fewer colonies from his flask and he would not get all 4.
What about the Ivins sample that didn’t test out? Which morphs if any did it have, how many colonies grown, etc.
How long have these morphs existed? How often do they form on their own? The same morphs are formed easily all the time? They all come from a single Ames lab source from 1981? Or other wild Ames has been added to lab stocks which had the morphs from hundreds or thousands of years ago?
If all lab Ames is from a single 1981 source, then wild Ames should have lots of different morphs. That could be tested.
==
.99^99 = .37
Suppose .5 taking into account error to see it.
1/2 for each of the 4. so 1/16.
and prob is under .01
of all 4 under .01
then say
.0025
.9975
1/4 * 1/100 * .9975
so more like 1/10 to see one.
in that case, its 1 in 10,000
.9975^99 = 0.78050831
16/1000
.0016^.25 = 0.2
so if it was .2 to see one of them, then
to see 4 is .0016 and out of 1000 labs that is 16.
.008^.25 = 0.299069756
.3
so if the chance to see one of the colonies is .3 per lab flask
then we get odds of 8/1000 to see all 4.
so out of 1000 flasks we get 8.
==
Suppose taking into account all factors, the percentage in the flask, the colonies grown, error in seeing the few morphs, the chance is .3 per morph per lab flask to see a morph. Then to see 4, one takes
.3^4 which is .0081. So out of 1000 labs, one finds all 4 8 times. In this case, all of the labs had the 4 morphs just only 8 detected them.
The total of all 4 morphs from the NYT article appears to be under 1 percent, so .25 percent each. This might work out to the .3 chance to see a morph depending on the number of colonies grown and accuracy to identify the few morphs.
==
number of colonies grown is likely random.
and multiple spore source is also random.
and may impact colony appearance. which one dominates if
different? or its unique?
==
actually, need to consider
1000, 4 type factor as well?
it should average out?
compute average and standard deviation.
average is
np?
==
the indels have been there since 1981 and
are the same in Wild Ames? they evolved thousands
of years ago.
think of how many would exist in the 1981 source
if 8 had evolved in 27 years.
if they evolved that fast in a few runs, then
evolution would have produced thousands of them in the
original Ames strain.
==
If 8 morphs had evolved from a single strain from 1981 and the 1981 had one only it doesn’t make sense. If 8 evolve in 20 years to 2001, then the 1981 Ames should have had many many indels already each producing different colonies. I.e. evolution should have produced more than 1 indel in some sample taken in 1981.
It makes more sense that the 8 were all there in 1981 and that the chance to see each morph and record it correctly is .3 per morph per lab flask, so that 8 were seen randomly. The letters were handled with more care and more colonies grown perhaps, so they identified those somewhat more accurately despite small fractions of the indels.
100bp = 1 percent = .01
1bp = .0001
= 1/10,000th
1ppm = .01 bp = .000001
the 4 morphs could be
.005,.003,.002,.001
ie 50bp,30bp,20bp,10bp
or
50bp, 10bp, 1bp, 1bp
or
5000ppm,1000ppm,100ppm,10ppm
if 1000 labs look at 1000 colonies that is 1 million colonies.
if a morph is in the frequency of 10ppm, then 10 labs see it
even though all have it.
If the original Ames sample was 10000 spores its a similar
set of statistics. If the Ames was taken from one cow infected
by a single spore then it could have a single morph. If
the Ames was taken from anthrax sourced from 1000 random spores, then its similar to 1000 colonies. However, random wild spores should have more indels since there has been a long time to create them. This can be tested against wild spores today.
There is also the question of the identification of these
colonies by sight. Is that science or make believe? Has the
method to identify colonies itself been tested? And all
1000 labs used such a method? Or its 1000 different people
looking at 1000 colonies each and making up their own rules
as to which colony is of a specified appearance?
==Following more repetitive rough notes including to some of the Meryl Nass posts
If you take anthrax powder and spread it out and grow it, isn’t it random which spores produce colonies? So some morphs in the sample don’t grow to colonies and some do? So it requires a statistical test? Looks like the entire procedure needs to be tested by going forward and then backward under controlled conditions. Also start with single flask or with multiple flasks with different morphs or overlapping morphs and see what happens.
Trillion spores anthrax only a few become colonies.
==
Each letter had about 1 trillion spores. So they didn’t grow 1 trillion colonies, they grew say 10 to 100 or 1000.
Suppose out of the 8 morphs mentioned at one point, each is present in a sample (flask or letter) in the amount of one percent each. If you grow 100 colonies from that flask or letter, then for those morphs you have a 1 in 100 chance to get it.
This applies to letters and to lab flasks. They had 1000 labs they tested? 8 had the 4 morphs they were checking for? If all 1000 labs had all 8 morphs but each lab grew 100 colonies per lab, then how many labs would have the 4 show up?
What if some labs grew 50 colonies? What is some grew 10? What if the Ivins flask, they grew 10,000 colonies and the other labs they grew 100 colonies?
There are quants from Lehman with nothing to do, why don’t they hire them to do Monte Carlo.
==
Maybe the 8 labs that found all 4 morphs were the 8 labs that grew 1000 or more colonies? The other labs grew fewer colonies? Monte Carlo was used at Los Alamos early on. Vahid Majidi is from Los Alamos.
We need a table of how many colonies grown by each lab and which morphs they found. We also need to know how many times they went back to grow more colonies from the Ivins flask until they got all 4 from that flask they were looking for, and whether they decided which of the 8 to look for after they concluded 4 were not in the Ivins flask.
==
compartmentalization helps you fix the science to the defendant.
Vahid has a good career ahead of him, on Wall Street.
Maybe the 8 labs that found all 4 morphs were the 8 labs that grew 1000 or more colonies? The other labs grew fewer colonies? Monte Carlo was used at Los Alamos early on. Vahid Majidi is from Los Alamos.
We need a table of how many colonies grown by each lab and which morphs they found. We also need to know how many times they went back to grow more colonies from the Ivins flask until they got all 4 from that flask they were looking for, and whether they decided which of the 8 to look for after they concluded 4 were not in the Ivins flask.
morph undel anthrax
how many spores produce a colony? one?
or multiple?
multiple inheritence so to speak.
the appearance? random walk or fractal or some
other stochastic complication?
unknown fractions of the undel dna in the
flasks and letters.
they don’t have the same frequency.
so number needed is variable.
==
“Though 99 percent of its spores were identical with the Ames ancestor, some 1 percent or less were morphs. “
” As the morphs became available, the F.B.I. started testing samples. At first, some had one or two of the morphs. None had three of the morphs.
By late 2005 to 2006 it became clear that just eight of the 1,070 samples collected included all four morphs.”
Because they started growing more colonies when they didn’t find all 4?
Let p[i][j] be the percentage of morph i in flask j. This is not a constant of nature. A flask can have a low percentage but still be there. If one grows 1000 colonies and p[i][j] is .01 in one flask and
.0001 in another, then you may not get it when testing that flask.
If a person was the bad guy he could just grow fewer colonies from his flask and he would not get all 4.
What about the Ivins sample that didn’t test out? Which morphs if any did it have, how many colonies grown, etc.
How long have these morphs existed? How often do they form on their own? The same morphs are formed easily all the time? They all come from a single Ames lab source from 1981? Or other wild Ames has been added to lab stocks which had the morphs from hundreds or thousands of years ago?
If all lab Ames is from a single 1981 source, then wild Ames should have lots of different morphs. That could be tested.
==
radiation causes the morphs? or what? stimulates them at
higher rate? based on what is going on in the lab, altitude,
etc?
stochastic appearance of a colony? multiple spore
origin of a colony?
other conditionds during growth, special appearance
depends on the indel and on one or more additional
factors?
==Possible Vahid Majidi responses:
Defense: We grow 1 million colonies per lab flask and use visual inspection.
Q: Did you take flasks that didn’t show colonies with the 4 morphs and see if they had the purported causal indels anyhow? This could look at whether other factors are needed in combination to produce the purported different shapes (morphs) or that the purported different shapes are just imaginary. Stochastic processes are known to fool humans by producing patterns that are random. Did you try to see if that was happening? If so how? How did you get data into computer files for statistical analysis if visual id was your method?
Richard Spencer on 23 Dec 2008 at 9:54 pm #
Well, I guess it’s kinda ironic that I’m leaving a comment (since I just banned them all at my site), but, yes, you’re right, the White Nats were the reason. Hopefully, we’ll be able to have good discussions of articles on The Sniper’s Tower.
R