Alex Crits-Christoph
@acritschristoph.bsky.social
Computational microbiologist
I like to post about: microbial genomics, microbial ecology, evolution, micro+plant biotechnology, climate, symbiosis, virology, ag, sci publishing and policy
I like to post about: microbial genomics, microbial ecology, evolution, micro+plant biotechnology, climate, symbiosis, virology, ag, sci publishing and policy
This was also all leading up to how outrageously bad this sentence is, which I was going to rag on, but the methods are so poor that it doesn't even state which assembler was used here, Table S2 contradicts it with no explanation of why, and also apparently only 4M reads were sequenced? Sigh.
November 16, 2025 at 5:30 PM
This was also all leading up to how outrageously bad this sentence is, which I was going to rag on, but the methods are so poor that it doesn't even state which assembler was used here, Table S2 contradicts it with no explanation of why, and also apparently only 4M reads were sequenced? Sigh.
Why do we have to go to github or supplementary table 2 to learn what the "recommended" method was (MetaPhlAn3)? And what about Lab 2, which also used it?
Why is there no attempt to understanding *why* these different methods give different results, as if they are unknown alien black boxes?
Why is there no attempt to understanding *why* these different methods give different results, as if they are unknown alien black boxes?
November 16, 2025 at 5:30 PM
Why do we have to go to github or supplementary table 2 to learn what the "recommended" method was (MetaPhlAn3)? And what about Lab 2, which also used it?
Why is there no attempt to understanding *why* these different methods give different results, as if they are unknown alien black boxes?
Why is there no attempt to understanding *why* these different methods give different results, as if they are unknown alien black boxes?
so...personally I think this is a very poor work which is really deeply confused about what metagenomics is, why we do it, and what the key biologically relevant biases actually are.
But, hey, I know there are deep divisions in the field which can't be overcome through micro-posts.
Key table:
But, hey, I know there are deep divisions in the field which can't be overcome through micro-posts.
Key table:
November 16, 2025 at 5:30 PM
so...personally I think this is a very poor work which is really deeply confused about what metagenomics is, why we do it, and what the key biologically relevant biases actually are.
But, hey, I know there are deep divisions in the field which can't be overcome through micro-posts.
Key table:
But, hey, I know there are deep divisions in the field which can't be overcome through micro-posts.
Key table:
Just send this to everyone who hasn't yet realized that these guys are groveling propagandists:
November 15, 2025 at 2:35 PM
Just send this to everyone who hasn't yet realized that these guys are groveling propagandists:
This is a really cool bacterial strain, happy to work on it!
One especially cool thing about P. sakaiensis is it consumes non-biodegradable PET plastic, it converts it into PHB (biodegradable) plastic.
Here's our conclusion on why we're working with this strain:
One especially cool thing about P. sakaiensis is it consumes non-biodegradable PET plastic, it converts it into PHB (biodegradable) plastic.
Here's our conclusion on why we're working with this strain:
November 12, 2025 at 7:05 PM
This is a really cool bacterial strain, happy to work on it!
One especially cool thing about P. sakaiensis is it consumes non-biodegradable PET plastic, it converts it into PHB (biodegradable) plastic.
Here's our conclusion on why we're working with this strain:
One especially cool thing about P. sakaiensis is it consumes non-biodegradable PET plastic, it converts it into PHB (biodegradable) plastic.
Here's our conclusion on why we're working with this strain:
We also performed a neat screen where you deliver a plasmid to the RB-TnSeq library, and select to enrich gene mutants with improved transformation efficiency. This is kind of similar to a recent approach by @cresslab.bsky.social and colleagues (www.biorxiv.org/content/10.1...)
November 12, 2025 at 7:05 PM
We also performed a neat screen where you deliver a plasmid to the RB-TnSeq library, and select to enrich gene mutants with improved transformation efficiency. This is kind of similar to a recent approach by @cresslab.bsky.social and colleagues (www.biorxiv.org/content/10.1...)
Very happy to share our recent work @cultivarium.bsky.social on genetic tools for Ideonella sakaiensis, a (Betaproteo-)bacterium that degrades PET plastic.
We identified a plasmid vector for the strain and generated a large RB-TnSeq library, screening for genes impacting plastic degradation.
We identified a plasmid vector for the strain and generated a large RB-TnSeq library, screening for genes impacting plastic degradation.
November 12, 2025 at 7:05 PM
Very happy to share our recent work @cultivarium.bsky.social on genetic tools for Ideonella sakaiensis, a (Betaproteo-)bacterium that degrades PET plastic.
We identified a plasmid vector for the strain and generated a large RB-TnSeq library, screening for genes impacting plastic degradation.
We identified a plasmid vector for the strain and generated a large RB-TnSeq library, screening for genes impacting plastic degradation.
Both are really freaking cool science
Absolutely loving these "unnatural constructs, genome-like patchworks of genes that have been stitched together into computer files by binning" (those who know, know)
Absolutely loving these "unnatural constructs, genome-like patchworks of genes that have been stitched together into computer files by binning" (those who know, know)
November 10, 2025 at 5:43 PM
Both are really freaking cool science
Absolutely loving these "unnatural constructs, genome-like patchworks of genes that have been stitched together into computer files by binning" (those who know, know)
Absolutely loving these "unnatural constructs, genome-like patchworks of genes that have been stitched together into computer files by binning" (those who know, know)
Amazing paper, especially love this figure of what differentiates broad host range phages: especially Diversity Generating Retroelements and multiple methyltransferases
November 7, 2025 at 3:01 AM
Amazing paper, especially love this figure of what differentiates broad host range phages: especially Diversity Generating Retroelements and multiple methyltransferases
oh no.... 2009 has been cancelled again
November 3, 2025 at 9:21 PM
oh no.... 2009 has been cancelled again
See ya folks, 2009 was a better place and I just got my invite to go back
November 3, 2025 at 9:20 PM
See ya folks, 2009 was a better place and I just got my invite to go back
To be fair, nyt, fox, cnn, cbs, and abc all did cover this story. But fundamentally, I do not understand how this is not bigger news. Even on The Crimson it's halfway down the page!
November 2, 2025 at 7:25 PM
To be fair, nyt, fox, cnn, cbs, and abc all did cover this story. But fundamentally, I do not understand how this is not bigger news. Even on The Crimson it's halfway down the page!
it's kind of hard to say when it's based on a couple cages of mice. It's the sort of thing that you'd want to see replicated. Not that it's noise, but that it's hard to control for in a single experiment: cage variability, unconscious biases, where the cages are in the room...
October 14, 2025 at 12:48 PM
it's kind of hard to say when it's based on a couple cages of mice. It's the sort of thing that you'd want to see replicated. Not that it's noise, but that it's hard to control for in a single experiment: cage variability, unconscious biases, where the cages are in the room...
The full language is even worse, asking to ban gene drives and microbes as well. Would exclude work like this on modified mosquitoes: www.npr.org/2024/01/26/1...
I love the IUCN, but also, they have no political authority, this is just a suggestion. Not a good one though!
I love the IUCN, but also, they have no political authority, this is just a suggestion. Not a good one though!
October 6, 2025 at 6:35 PM
The full language is even worse, asking to ban gene drives and microbes as well. Would exclude work like this on modified mosquitoes: www.npr.org/2024/01/26/1...
I love the IUCN, but also, they have no political authority, this is just a suggestion. Not a good one though!
I love the IUCN, but also, they have no political authority, this is just a suggestion. Not a good one though!
For a week now the harbor has been bright green and half of Baltimore has smelled like rotten eggs.
Most likely, this is a Chlorobi bloom!
Chlorobi are anoxygenic photosynthetic green sulfur bacteria brought up from the bottom of the harbor by warm waters aqua.org/stories/2023...
Most likely, this is a Chlorobi bloom!
Chlorobi are anoxygenic photosynthetic green sulfur bacteria brought up from the bottom of the harbor by warm waters aqua.org/stories/2023...
October 6, 2025 at 1:21 PM
For a week now the harbor has been bright green and half of Baltimore has smelled like rotten eggs.
Most likely, this is a Chlorobi bloom!
Chlorobi are anoxygenic photosynthetic green sulfur bacteria brought up from the bottom of the harbor by warm waters aqua.org/stories/2023...
Most likely, this is a Chlorobi bloom!
Chlorobi are anoxygenic photosynthetic green sulfur bacteria brought up from the bottom of the harbor by warm waters aqua.org/stories/2023...
30% of Americans said they knew nothing about Kennedy's impacts! But those who were aware overwhelmingly thought they were bad. Including 41% vs 16% of independents.
Kennedy's policies are uniquely unpopular as policies go in American politics, even if they are popular on X. Tell people about them!
Kennedy's policies are uniquely unpopular as policies go in American politics, even if they are popular on X. Tell people about them!
September 25, 2025 at 3:49 PM
30% of Americans said they knew nothing about Kennedy's impacts! But those who were aware overwhelmingly thought they were bad. Including 41% vs 16% of independents.
Kennedy's policies are uniquely unpopular as policies go in American politics, even if they are popular on X. Tell people about them!
Kennedy's policies are uniquely unpopular as policies go in American politics, even if they are popular on X. Tell people about them!
At 88%, it's hard to find a topic that more Americans agree with each other on than the benefits of routine vaccinations. And with 62% for COVID vaccines (while sadly low), that is also something of a supermajority consensus as policies go in American politics
www.pewresearch.org/science/2023...
www.pewresearch.org/science/2023...
September 25, 2025 at 3:49 PM
At 88%, it's hard to find a topic that more Americans agree with each other on than the benefits of routine vaccinations. And with 62% for COVID vaccines (while sadly low), that is also something of a supermajority consensus as policies go in American politics
www.pewresearch.org/science/2023...
www.pewresearch.org/science/2023...
Useful polling data: In 2025, confidence in public health institutions has steeply declined among Democrats, but hasn't gained under Republicans. MAHA public health takeovers appear very unconvincing, even to supporters.
www.annenbergpublicpolicycenter.org/public-confi...
(h/t @tgof137.bsky.social)
www.annenbergpublicpolicycenter.org/public-confi...
(h/t @tgof137.bsky.social)
September 24, 2025 at 2:09 PM
Useful polling data: In 2025, confidence in public health institutions has steeply declined among Democrats, but hasn't gained under Republicans. MAHA public health takeovers appear very unconvincing, even to supporters.
www.annenbergpublicpolicycenter.org/public-confi...
(h/t @tgof137.bsky.social)
www.annenbergpublicpolicycenter.org/public-confi...
(h/t @tgof137.bsky.social)
Yeah, I think the data from KFF is helpful here
www.kff.org/health-infor...
That said, while scientists and their institutions are well-trusted, of course we should also try to explain their scientific reasoning as well! Look to those on here with a track record of doing so for guidance IMO
www.kff.org/health-infor...
That said, while scientists and their institutions are well-trusted, of course we should also try to explain their scientific reasoning as well! Look to those on here with a track record of doing so for guidance IMO
September 23, 2025 at 4:56 PM
Yeah, I think the data from KFF is helpful here
www.kff.org/health-infor...
That said, while scientists and their institutions are well-trusted, of course we should also try to explain their scientific reasoning as well! Look to those on here with a track record of doing so for guidance IMO
www.kff.org/health-infor...
That said, while scientists and their institutions are well-trusted, of course we should also try to explain their scientific reasoning as well! Look to those on here with a track record of doing so for guidance IMO
And then where are these new mutations from? They could be from other related phage, just not found in the best hit? That's Fig 4F. Indeed many of the new mutations are found in other close relatives. Especially, I think, for competition winners like #69 and #100 (unless I am reading this wrong!)
September 18, 2025 at 1:33 PM
And then where are these new mutations from? They could be from other related phage, just not found in the best hit? That's Fig 4F. Indeed many of the new mutations are found in other close relatives. Especially, I think, for competition winners like #69 and #100 (unless I am reading this wrong!)
Great and nuanced thread. But I think we can expand further. As noted, phage selected for synthesis, and that worked, were significantly less novel.
In Fig 4D, there's a very strong correlation between novelty and not working. The phage that worked were much less novel. This is nucleotide ID!
In Fig 4D, there's a very strong correlation between novelty and not working. The phage that worked were much less novel. This is nucleotide ID!
September 18, 2025 at 1:33 PM
Great and nuanced thread. But I think we can expand further. As noted, phage selected for synthesis, and that worked, were significantly less novel.
In Fig 4D, there's a very strong correlation between novelty and not working. The phage that worked were much less novel. This is nucleotide ID!
In Fig 4D, there's a very strong correlation between novelty and not working. The phage that worked were much less novel. This is nucleotide ID!
The Wall Street Journal Opinions section is not a platform on which meaningful or good-faith discussion of science publishing can or should occur.
It is emblematic of the actual real world (and potentially existential!) challenges of science publishing and communication
grist.org/climate-skep...
It is emblematic of the actual real world (and potentially existential!) challenges of science publishing and communication
grist.org/climate-skep...
September 17, 2025 at 1:06 PM
The Wall Street Journal Opinions section is not a platform on which meaningful or good-faith discussion of science publishing can or should occur.
It is emblematic of the actual real world (and potentially existential!) challenges of science publishing and communication
grist.org/climate-skep...
It is emblematic of the actual real world (and potentially existential!) challenges of science publishing and communication
grist.org/climate-skep...
If your desktop never looked like this in 2010 you missed out on the most rad time in UI and sadly you may never get the chance again
September 14, 2025 at 2:41 PM
If your desktop never looked like this in 2010 you missed out on the most rad time in UI and sadly you may never get the chance again
The new -outfmt 20 in BLAST 😍. No more frustrated googling to remember which column is which.....
September 6, 2025 at 2:54 PM
The new -outfmt 20 in BLAST 😍. No more frustrated googling to remember which column is which.....
What a figure!
September 3, 2025 at 12:41 AM
What a figure!