Final Exam - AG

• Themes


  • Similar to ones we've seen
  • Will be more molecular
  • Non-adaptive evolution
  • Human genetics
  • Ethical issues
  • Breaking the rules
• The tardigrade genome scandal

  • Water bears
  • This organism and scandal ties together some pillars of the course
  • Pressure to publish and race for high impact publications
  • Bioinformatics and genomics (genome assembly and where things can go wrong)
• Don't air your dirty genome assemblies in public
• Another big theme is when our expectations overpower the data
• Scientific fraud


  When someone fudges the data
• Sometimes scientists aren't out to cheat or fudge data but really want to believe what they see is true
• It's easy to convince yourself what you're analyzing is true
• Organism superhero


  • The superman of biology, what would we create?
  • How would we structure its genome?
  • It's the tardigrade
  • Found everywhere
  • Mountain top deep sea mud volcano
  • Very resilient
  • Can survive extreme temps and space, air deprivation, radiation
  • They're animals
  • It falls in the broad group of arthropods and nematodes
  • It is super tough and cool
  • It makes sense why we would want to study its genome and wonder why it evolved these remarkable capabilities
• All these other things are cool but not really so something happened in the DNA lineage providing them these capabilities or something came in horizontally to give them these abilities
• The first assembly of a tardigrade genome

  • What they argued was not a lot of interesting changes from ancestors but remarkable help from the outside with HGT
  • Mashed up tardigrade got DNA generated contigs and analyzed them
  • Found that a lot of the genes in their contigs and scaffolds hit to other organisms not anywhere near the evolutionary tree to tardigrades
  • Essentially they had a structural annotation and then gone to the functional annotation and search database to find matches
  • Most of their gene models they are searching against the database will hit to closely related organisms
  • But what they did find was that some of their gene models were hitting to weird things like plants
  • They estimate that approximately one-sixth of tardigrade genes entered by HGT, nearly double the fraction found in the most extreme cases of HGT into animals known to date
  • They basically said they broke the record for HGT
  • So they were really excited about this story
• In biology and genetics there's fads
• HGT


  Has become a big fad in the world of genetics
• Another one was epigenetics
• Evidence for extensive HGT for draft genome of a tardigrade


  • This paper grabbed major attention
  • Tardigrades often live in wet environments and eat algae, fungi etc.
  • When you isolate DNA from tardigrade you probably get some of the DNA from the environment as well
  • When sequencing you work with total cellular DNA and these machines don't discriminate
  • So basically what happened when they sequenced all this DNA they also sequenced some of their food and environment… so embarrassing
• Some scientists began to figure out that their work was a little bit sloppy
• Literally 5 months after, they put a paper in the SAME journal about how they were wrong LMAO
• They flamed them
• Basically realized first paper fucked up so bad
• They found basically no functional HGT
• You'll see there is a see commentary section
• If we look at the first paper we can write a letter to PNAS which thinks they fucked up and it gives you a publication in PNAS
• After the second genome

  • There was two letters to the editor
  • The letters are arguing against the first genome
  • Did their own analysis and basically found little evidence for HGT
  • This one team went through the contigs of the first paper and one contig was literally a whole bacterial chromosome (so embarrassing)
• The response


  • The first team came back with a rebuttal
  • The wrote a letter saying they may have screwed up but they stand by their findings
  • Basically they said they submitted the wrong assembly lol (liars)
  • They purged contamination and uploaded the new one
  • They submitted a formal correction to their paper with the new assembly and played down the amount of HGT by a significant amount but still stand by the HGT story
• The paper never did get withdrawn and still has a lot of citation
• The second genome only has 254 citations
• The letters did pretty good for citations too
• One letters did not that the counterarguments exemplify the success of open science and sequencing data
• The saga continues, still sequencing tardigrade genomes
• Resequencing species and looking at the same genome HGT doesn't appear to be a huge source of the cool genome
• In the world as a whole there's a lot of divisive topics
• Most hard science isn't too divisive
• What would get a lot of people arguing is junk DNA


  • It brings out the anger of a lot of geneticists
  • Some believe it is junk some believe there is no junk DNA and think that term is inappropriate
• Ideology


  Ideological divide in those who believe in junk DNA and those who don't
• The lecture is built around a manuscript called 'on causal roles and selected effects our genome is mostly junk'
• The dude who wrote it edited the tardigrade scandal
• The prof interacted with Doolittle
• He won Canada's Nobel prize from NSERC
• Ford's start to becoming a famous scientist started back in 1980 where Nature published two letter simultaneously
• One paper was Ford and one was Watson and Crick
• These teams both discovered selfish DNA (intimately tied with junk DNA)