4 ms·

I've always said it's not the Tree of Life, but rather the DAG of Life.

User23 5y ago
It may not even be acyclic. For example it appears fetal DNA is permanently detectable in mothers and may even have health benefits that conceivably increase the mother’s evolutionary fitness.
- jfarmer 5y ago
  The hypergraph of life?
  - taliesinb 5y ago
    Yup. Genetic recombination means some genotypes are the result of crossover of two parents. Horizontal gene transfer has a similar implication. This means the true structure is a directed hypergraph.
- westurner 5y ago
  How can it be acyclic? A phylogenetic tree is a DAG. Organisms sharing DNA? That's definitely a cyclic graph. If there were Schema.org/Animal and/or schema:AnimalInstance classes, what do you list under a :breed property to indicate that e.g. one parent is breed X and another is breed Y?! That's definitely not a DAG; that looks like a feature clustering dendrogram. DNA barcoding > Mismatches between conventional (morphological) and barcode based identification https://en.wikipedia.org/wiki/DNA_barcoding#Mismatches_between_conventional_(morphological)_and_barcode_based_identification https://en.wikipedia.org/wiki/DNA_barcoding#Mismatches_betwe... Taxonomy (biology) https://en.wikipedia.org/wiki/Taxonomy_(biology) https://en.wikipedia.org/wiki/Taxonomy_(biology) FWIU, there's at least one DNA-based organism naming system; IDK how much that helps resolve :Animal and :AnimalInstance if at all?
  - sixstringtheory 5y ago
    My assumption as someone not formally trained in advanced biology is that the phylogenetic tree has an implied arrow of time, and each node of the tree is a point where a mutation occurred that was sufficient to create a new and separate family/order/genus/etc afterwards, with leaf nodes representing species. In this sense a cycle can’t occur because a branch would need to reach back in time and rejoin with an ancestral branch. It would be a different kind of grandfather paradox: who would be the ancestor and who the descendant in a cycle? Maybe someone could help point out the flaws in this model.
    - flobosg 5y ago
      Your assumption is true, but only for rooted phylogenetic trees. In unrooted trees the node representing the most ancestral state is absent and thus no directionality can be determined.
agumonkey 5y ago
I'd go full mad and say the space continuum of life. Context is what drives life. Similar context breed similar forces and genes.
- Swizec 5y ago
  > Similar context breed similar forces and genes Flight is so useful, it evolved 4 times independently. With very similar solutions. https://en.wikipedia.org/wiki/Flying_and_gliding_animals https://en.wikipedia.org/wiki/Flying_and_gliding_animals And crustaceans keep evolving into crabs. https://www.popsci.com/story/animals/why-everything-becomes-crab-meme-carcinization/ https://www.popsci.com/story/animals/why-everything-becomes-... And who even knows how many different times high level intelligence has evolved. I think octopi, birds, and mammals are all good examples of separate intelligence tracks with similar results.
  - agumonkey 5y ago
    I believe Darwin envisioned that, and the Tree of Evolution was just an introductory notion (I never read his book) before going into subtler reasons for new traits.

It may not even be acyclic. For example it appears fetal DNA is permanently detectable in mothers and may even have health benefits that conceivably increase the mother’s evolutionary fitness.

jfarmer 5y ago
The hypergraph of life?
- taliesinb 5y ago
  Yup. Genetic recombination means some genotypes are the result of crossover of two parents. Horizontal gene transfer has a similar implication. This means the true structure is a directed hypergraph.
westurner 5y ago
How can it be acyclic? A phylogenetic tree is a DAG. Organisms sharing DNA? That's definitely a cyclic graph. If there were Schema.org/Animal and/or schema:AnimalInstance classes, what do you list under a :breed property to indicate that e.g. one parent is breed X and another is breed Y?! That's definitely not a DAG; that looks like a feature clustering dendrogram. DNA barcoding > Mismatches between conventional (morphological) and barcode based identification https://en.wikipedia.org/wiki/DNA_barcoding#Mismatches_between_conventional_(morphological)_and_barcode_based_identification https://en.wikipedia.org/wiki/DNA_barcoding#Mismatches_betwe... Taxonomy (biology) https://en.wikipedia.org/wiki/Taxonomy_(biology) https://en.wikipedia.org/wiki/Taxonomy_(biology) FWIU, there's at least one DNA-based organism naming system; IDK how much that helps resolve :Animal and :AnimalInstance if at all?
- sixstringtheory 5y ago
  My assumption as someone not formally trained in advanced biology is that the phylogenetic tree has an implied arrow of time, and each node of the tree is a point where a mutation occurred that was sufficient to create a new and separate family/order/genus/etc afterwards, with leaf nodes representing species. In this sense a cycle can’t occur because a branch would need to reach back in time and rejoin with an ancestral branch. It would be a different kind of grandfather paradox: who would be the ancestor and who the descendant in a cycle? Maybe someone could help point out the flaws in this model.
  - flobosg 5y ago
    Your assumption is true, but only for rooted phylogenetic trees. In unrooted trees the node representing the most ancestral state is absent and thus no directionality can be determined.

agumonkey 5y ago

I'd go full mad and say the space continuum of life. Context is what drives life. Similar context breed similar forces and genes.

Swizec 5y ago
> Similar context breed similar forces and genes Flight is so useful, it evolved 4 times independently. With very similar solutions. https://en.wikipedia.org/wiki/Flying_and_gliding_animals https://en.wikipedia.org/wiki/Flying_and_gliding_animals And crustaceans keep evolving into crabs. https://www.popsci.com/story/animals/why-everything-becomes-crab-meme-carcinization/ https://www.popsci.com/story/animals/why-everything-becomes-... And who even knows how many different times high level intelligence has evolved. I think octopi, birds, and mammals are all good examples of separate intelligence tracks with similar results.
- agumonkey 5y ago
  I believe Darwin envisioned that, and the Tree of Evolution was just an introductory notion (I never read his book) before going into subtler reasons for new traits.