Sandwalk

These guys do think LUCA was at a hydrothermal ven...

2026-08-10T10:08:34.723-04:00

These guys do think LUCA was at a hydrothermal vent, and the metabolic enzymes people have traced back to LUCA do support that hypothesis. Anything with translation was certainly alive, and they aren't claiming otherwise. They aren't saying LUCA was nonliving because it used metals instead of enzymes to catalyze certain reactions, they're saying that the environment already provided the catalysts for those reactions so enzymes would have been redundant until life escaped the hydrothermal vents. You're correct that they conspicuously don't address the origin of the central dogma, which in my view is a major blindspot of the metabolism-first hypothesis, but it's not like anyone else has gotten much closer besides showing that the ribosome is (mostly) a ribozyme.

That's hilarious, they did not say anything li...

2026-08-10T09:59:02.991-04:00

That's hilarious, they did not say anything like that. In fact, they said that a competing hypothesis requires two origins of metabolism as a criticism. I suspect the popsci misinformation is AI or NS- hallucinated from this line: "Cyanide-dependent synthesis thus requires two origins of metabolism, one from cyanide and the modern version from CO2."

Larry, thanks for bringing this paper up. What m...

2026-08-10T03:20:43.981-04:00

Larry, thanks for bringing this paper up.

What makes the whole story confusing is that the authors switch back and forth from 'phosphorylating hydrothermal vents' to LUCA, bacteria, and everything in between. For example "We show that enzymatic metabolism in the universal common ancestor was incomplete," but the universal common ancestor didn't live in a phosphorylating hydrothermal vent?! so that is not the origin of life... LUCA: Bacteria, and Archaea are living cellular organisms. But whatever was present at ''phosphorylating hydrothermal vents' can not be called 'life' isn't it? cellular organisms at phv's?

quote:
"At the origin of metabolism, there were no enzymes"
I fully agree! but that means: no ribosomes, no RNA, no DNA. I miss the orgin of a full genetic system

quote:
"We show that enzymatic metabolism in the universal common ancestor was incomplete," OK, that's interesting and new (?), but that is not the origin of life...!?

Larrry, you wrote "Over time, the inorganic catalysts were gradually replaced by protein and RNA catalysts ..."
but as soon as you introduce "protein and RNA catalysts" you assume a full DNA based information system with a genetic code, mRNA, tRNA, rRNA and ribosomes...
"gradually replaced": That is easy to say, but those enzymatic proteins must be developed from from scratch, out of nothing, isn't it? because there was no genetic system at the time of non-enzymatic catalysis... So, I think that problem is glossed over too easily.

You are right that authors should address all of the criticisms and problems with their hypotheses, but first their goals must be stated clearly, what is the problem they try to solve, and do they present data that match their goals? Do they stay focused? is their story unnecessary complicated?

This is being spun in the press as two separate or...

2026-08-10T00:18:52.408-04:00

This is being spun in the press as two separate origins of life, which requires the assumption that the LUCA was not living. Are the authors or their university encouraging that view in any way?

Thanks for discussing this intriguing paper. What ...

2026-08-09T13:00:03.498-04:00

Thanks for discussing this intriguing paper. What does Nick Lane say?

Thank you for presenting the current studies.

2026-08-08T22:06:47.714-04:00

Thank you for presenting the current studies.

I love that restaurant TH

2026-08-08T08:31:57.944-04:00

I love that restaurant TH

Based strictly on spatial geometry, if an organic ...

2026-08-06T16:20:17.185-04:00

Based strictly on spatial geometry, if an organic chemist took unesterified sn-glycerol-1-phosphate and renumbered the carbon chain from the opposite end using standard IUPAC non-stereospecific nomenclature, which classical Fischer projection naming convention (D-glycerol or L-glycerol derivative) corresponds to the Archaeal sn-G1P backbone?

Show your step-by-step spatial derivation of the carbon chain priority.

My fountain family is related to Abraham Rycker ...

2026-08-04T08:37:51.020-04:00

My fountain family is related to Abraham Rycker and am glad to learn how the French Dutch German connection.

Betts was dismissed from the QR at the same time a...

2026-07-21T15:40:30.278-04:00

Betts was dismissed from the QR at the same time as Colonel Rogers. That is way too early to ever have been under the command of Arnold.

George Washington is my 4th cousin 4x removed thro...

2026-07-21T15:33:16.829-04:00

George Washington is my 4th cousin 4x removed through Dr. Betts' (my 4th ggf) mother, Mary Belding.

I wonder how many students actually use textbooks ...

2026-06-26T02:56:37.698-04:00

I wonder how many students actually use textbooks today. My university has installed some AI tool in which they can feed pdfs of our lectures. It sumarizes them and develops questions they can use for learning. I don't know if this really works but I guess there is no way back.

Wouldn't it be nice if research scientists, po...

2026-06-21T15:54:46.982-04:00

Wouldn't it be nice if research scientists, postdocs, and graduate student read a reputable textbook from time to time?

continuing the quote from Alberts et al. 7th ed. (...

2026-06-21T15:53:34.248-04:00

continuing the quote from Alberts et al. 7th ed. (p. 231)

"As previously stated, there is a strong scientific consensus that most of the human genome consists of DNA whose nucleotide sequence is not relevant to biological function - being so-called junk. This conclusion rests on the finding that natural selection fails to preserve these sequences in the face of the inevitable random changes to genomes that occur over time, as can be seen both when different species are compared and from detailed analyses of human variation. The fact that these DNA sequences nevertheless produce an occasional RNA molecule can be explained by the occurrence of background "noise" in gene expression. Although gene expression is very accurate, it is not perfect, and biochemical errors occasionally occur. Such errors are to be expected, and so long as they are kept at a low level, they are thought to have little or no consequence for the cell."

@Lantog I help a bit on the last (7th) edition of...

2026-06-21T15:44:22.150-04:00

@Lantog

I help a bit on the last (7th) edition of Alberts. (Bruce Alberts was my Ph.D. supervisor.) Here's what they say on page 230.

"The first obstacle in interpreting the sequence of the 3.1 billion nucleotide pairs in the human genome is the fact that the nucleotide sequence of most of it (about 90%) is probably functionally unimportant."

"... The important question of how much of the DNA sequence of the human genome is functionally important was briefly confused by a set of high-profile publications that appeared in 2012 from a large, federally funded US genome project named ENCODE. These publications, which reported the results of a massive survey using sensitive assays that can detect the presence of RNA molecules in cells at extremely low levels, reported that 76% of the total DNA sequence in human cells is transcribed to produce RNA molecules. Even though many of these transcripts were found at levels of less than a single RNA molecule per cell, the ENCODE scientists used such data to assert that most of human DNA is functional, with very little "junk." This claim received widespread publicity, along with their belief that our genome contains tens of thousands of previously undetected genes that produce RNA molecules that do not code for protein."

The current edition of Alberts is cautious on the ...

2026-06-21T11:26:49.393-04:00

The current edition of Alberts is cautious on the 80% functional claim. I was a reviewer for the previous edition of Lodish and suggested they pull back some of their previous claims. The next edition will be 1-2 years so we’ll see

I’m starting to think that you and Joe should foll...

2026-06-21T11:20:20.727-04:00

I’m starting to think that you and Joe should follow up on every example of this you see coming from scientists and write them a long referenced explanation on why they should be cautious in their claims. Over time this effort might have an impact

I agree that they aren't lying, and the fact t...

2026-06-21T10:00:47.784-04:00

I agree that they aren't lying, and the fact that they aren't lying is shameful to the scientific community. Imagine if exoplanet researchers declared that every planet in the universe is habitable just because we found some planets with water on them. That's where we are with the disaster of adaptationism in biology. Personally, my theory is that it's a combination of adaptationism and fetishization of complexity. Biologists are so obsessed with declaring how complex everything is that they assume that just because something happens in a cell it must be part of some mysterious super important unknown pathway that ignorant biologists of the past would have just called "junk". Even if you do a knockout experiment and show it doesn't matter they'll try to rationalize it as being used for some special cell type, life stage, or environment, which is fair enough as a hypothesis, but they take the mere possibility of a function as proof of a function to the point that it's unfalsifiable.

Two points: It's not lying if you believe it. ...

2026-06-20T14:18:20.354-04:00

Two points: It's not lying if you believe it. And it's not misrepresenting the facts, exactly; it's drawing unwarranted conclusions from a biased sample, e.g. finding a few functional TEs and claiming that therefore all TEs are functional.

@John Harshman In my opinion, there's a differ...

2026-06-19T18:13:07.151-04:00

@John Harshman
In my opinion, there's a difference between hype and lies. This Cell paper crosses the line and misrepresents the facts and that's lying. I think the Amgen scientists are also misrepresenting the facts.

Back about 1980, when everyone started saying they...

2026-06-19T14:33:12.298-04:00

Back about 1980, when everyone started saying they were introducing a New Paradigm, I decided that I would become unique among scientists of my generation by being the only one doing Normal Science.

Or perhaps it's typical science hype: your wor...

2026-06-19T13:19:17.992-04:00

Or perhaps it's typical science hype: your work is so much more important and tenure-worthy if it revolutionizes our understanding of the world.

Obviously because it's stimulating, controvers...

2026-06-18T23:16:11.393-04:00

Obviously because it's stimulating, controversial, and because all true molecular biologists and genomicists know it's got to be true -- except for a small percentage of them who are evolutionary types.

How/Why did Cell publish that?

2026-06-18T22:58:25.685-04:00

How/Why did Cell publish that?

That “Anonymous” was me, Joe Felsenstein.6

2026-06-18T18:24:51.812-04:00

That “Anonymous” was me, Joe Felsenstein.6