Wednesday, May 15, 2019

"Eukaryogenesis, how special really?"

Eukaryogenesis, how special really?

Another interesting article.


Eukaryogenesis is widely viewed as an improbable evolutionary transition uniquely affecting the evolution of life on this planet. However, scientific and popular rhetoric extolling this event as a singularity lacks rigorous evidential and statistical support. Here, we question several of the usual claims about the specialness of eukaryogenesis, focusing on both eukaryogenesis as a process and its outcome, the eukaryotic cell. We argue in favor of four ideas. 

  • First, the criteria by which we judge eukaryogenesis to have required a genuinely unlikely series of events 2 billion years in the making are being eroded by discoveries that fill in the gaps of the prokaryote:eukaryote “discontinuity.”
  • Second, eukaryogenesis confronts evolutionary theory in ways not different from other evolutionary transitions in individuality; parallel systems can be found at several hierarchical levels.
  • Third, identifying which of several complex cellular features confer on eukaryotes a putative richer evolutionary potential remains an area of speculation: various keys to success have been proposed and rejected over the five-decade history of research in this area.
  • Fourth, and perhaps most importantly, it is difficult and may be impossible to eliminate eukaryocentric bias from the measures by which eukaryotes as a whole are judged to have achieved greater success than prokaryotes as a whole. 

Overall, we question whether premises of existing theories about the uniqueness of eukaryogenesis and the greater evolutionary potential of eukaryotes have been objectively formulated and whether, despite widespread acceptance that eukaryogenesis was “special,” any such notion has more than rhetorical value.

Context: reading of David Quammen's "The Tangled Tree: A Radical New History of Life".

Tuesday, May 14, 2019

Peak Gene

Interesting article.

We have reached peak gene, and passed it.
Ken Richardson in "It's The End Of The Gene As We Know It" 

In scientific, as well as popular descriptions today, genes “act,” “behave,” “direct,” “control,” “design,” “influence,” have “effects,” are “responsible for,” are “selfish,” and so on, as if minds of their own with designs and intentions.

But at the same time, a counter-narrative is building, not from the media but from inside science itself.... Scientists now understand that the information in the DNA code can only serve as a template for a protein. It cannot possibly serve as instructions for the more complex task of putting the proteins together into a fully functioning being, no more than the characters on a typewriter can produce a story.
First, laboratory experiments have shown how living forms probably flourished as “molecular soups” long before genes existed. They self-organized, synthesized polymers (like RNA and DNA), adapted, and reproduced through interactions among hundreds of components. That means they followed “instructions” arising from relations between components, according to current conditions, with no overall controller: compositional information, as the geneticist Doron Lancet calls it.
In this perspective, the genes evolved later, as products of prior systems, not as the original designers and controllers of them. More likely as templates for components as and when needed: a kind of facility for “just in time” supply of parts needed on a recurring basis.
We have traditionally thought of cell contents as servants to the DNA instructions. But, as the British biologist Denis Noble insists in an interview with the writer Suzan Mazur, “The modern synthesis has got causality in biology wrong … DNA on its own does absolutely nothing until activated by the rest of the system … DNA is not a cause in an active sense. I think it is better described as a passive data base which is used by the organism to enable it to make the proteins that it requires.”

PS: the proposed definition of "gene" by Portin and Wilkins:
A gene is a DNA sequence (whose component segments do not necessarily need to be physically contiguous) that specifies one or more sequence-related RNAs/proteins that are both evoked by Genetic Regulatory Networks and participate as elements in Genetic Regulatory Networks, often with indirect effects, or as outputs of Genetic Regulatory Networks, the latter yielding more direct phenotypic effects.
Wiki tells us: genetic regulatory network (GRN) is a collection of molecular regulators that interact with each other and with other substances in the cell to govern the gene expressionlevels of mRNA and proteins.  

Monday, April 08, 2019

H.Res.109 - The Green New Deal

Friday, April 05, 2019

Arya per Sita in the Ramayana

Dholavira Seal from the Harappan Era.  No implication that this is connected to the story below. I just like it as an illustration.

 Aravindan Neelakandan reminds us:

In Ramayana, the Rakshasas are a group of people who were not, as many consider, uncultured, demonic people. Rather, they considered themselves superior to other humans and animals. In fact, when Ravana asked for the boon of invincibility from the creator Deity, he left out humans and animals because he thought they were too inferior to be bothered about.

The Rakshasa women who guarded Sita when she was being held captive were instructed by Ravana to torment Sita endlessly. Their taunts and threats even led Sita to contemplate suicide. But for the timely intelligent intervention of Hanuman - a Vanara emissary from Rama, she would have succumbed to the thought of suicide.

Now Rama had vanquished Ravana with the help of the Vanaras - the monkeys or the non-human primates. Hanuman was here to tell Sita the good news. Then he looked at all those Rakshasa women who had tormented her. He asked her permission to punish them.

Sita refused him to give permission but then told Hanuman what a bear once told a tiger.

This story told by Sita is known throughout India for millennia now . It is about how a hunter chased by a tiger in a forest, escaped by climbing a tall tree. In the tree was a bear. The tiger told the bear that the hunter is the killer of wild animals and hence the bear should push him down. The bear refused. He said that the tree being the home of the bear, the hunter had become its guest. And it was the dharma of the householder to protect the guest.
The tiger waited. Soon, the bear fell asleep. The tiger told the man that despite the grand words, the bear was actually reserving the man for himself. So, the tiger suggested that if the man pushed the bear down, then the tiger could easily devour and eat the sleepy bear and would go its way while the man too could be free of danger. The hunter yielded to the temptation and pushed the bear down. The bear, adept in living on the trees, saved itself.

Now the tiger appealed again to the bear. Pointing out the treachery of the man it asked him to push him down. The bear told the tiger that a noble person does not do evil deeds to revenge evil deeds. A good person, he said, always does good deeds irrespective of what the others do. After saying this, Sita defined the term ‘Arya’ in a very famous statement:

Kaaryam kaarunyamaaryen na kashchit naaparaadhyati
(कार्यं कारुण्यमार्येण न कश्चिन्नापराध्यति) :
Showing kindness (towards the saintly and the sinner alike) defines a person as Arya for there is none who has never committed a wrong.

Valmiki Ramayana: Yuddha Kanda: 46

Here, the term ‘Arya’, much maligned by colonial Indology, European historiography and Nazi racism , is defined as a quality that is even above mercy, compassion and empathy combined, possessed not only by humans but by all living beings. Only a being who possesses that quality irrespective of what species it belongs to, should be considered as noble - ‘Arya’. Thus defined Sita the term ‘Arya’.

Monday, March 25, 2019

India - a growing discontent?

There is an outfit that publishes the World Happiness Report.  The primary measure is the "Cantril Life Ladder" (from Hadley Cantril, Patterns of Human Concern, 1965).

As far as I can tell, some 1000-odd people of age 15+  in each of 156 to 158 countries are asked by Gallup polling each year the following question, which in English reads:
“Please imagine a ladder, with steps numbered from 0 at the bottom to 10 at the top. The top of the ladder represents the best possible life for you and the bottom of the ladder represents the worst possible life for you. On which step of the ladder would you say you personally feel you stand at this time?”
The average for the country is supposed to reflect its level of happiness.   The Cantril Life Ladder is available for India from 2006 onwards.  The report also includes measures that one might think affects the answers given on the Cantril Life Ladder, such as per capita income and life expectancy, and survey measures such as perceived freedom to make life choices, perceived corruption, and so on.  India is generally improving on these measures over the 2006-2018 time period.  One interesting thing is that countries with poorer improvement on these measures can be happier than India.

Friday, March 22, 2019

NYT Magazine: Is Ancient DNA Research Revealing New Truths?

I am told that this article is worth reading: "Is Ancient DNA Research Revealing New Truths — or Falling Into Old Traps?"
Maybe some time I will.

Saturday, February 16, 2019

On Graduate School

For a graduate student it can be very difficult. It’s very easy to get discouraged if you have no real understanding that you’re going to be stuck for a very long time.

I could very easily have imagined myself getting discouraged and dropping out of graduate school. That could have easily happened to me under different circumstances.

Graduate school is a different environment and then you start to wonder—“Am I really good enough to do research-level math?” It’s hard, in fact, to tell. You see all these people who are doing great things around you and then you think, well, maybe you’re not cut out for this. So I think it’s important [long pause] to have someone who believes in you.
from an interview with Akshay Venkatesh.

Akshay Venkatesh in the news.