Some interesting stuff/citations/thoughts I like …

Oh great, now I’m worse than a fraud … practically a biologist

— Dr. Sheldon Cooper, Ph.D., Sc.D. ( a fictional character of THE BIG BANG THEORY sitcom)

I have taken a stand against atheism because I am convinced that it is perilously built on false premises and misinterpretations of evidence. . . . Properly understood, the evidence inexorably points to the existence of a creator God.

— Professor John Lennox (Mathematician, University of Oxford)

When you look at the narrative for hominin origins, it’s just a big mess — there’s no consensus whatsoever … People are working under completely different paradigms, and that’s something that I don’t see happening in other fields of science

— Sergio Almécija (a senior research scientist in the American Museum of Natural History’s Division of Anthropology)

There’s no reason to doubt that Darwin successfully explained the small adjustments by which an organism adapts to local circumstances: changes to fur density or wing style or beak shape. Yet there are many reasons to doubt whether he can answer the hard questions and explain the big picture—not the fine-tuning of existing species but the emergence of new ones. The origin of species is exactly what Darwin cannot explain.

— Professor David Gelernter (Computer science, Yale University)

Where is Anatomy Encoded in Living Systems?

Biologists don’t love to think about goal directed processes, the idea is there supposed to be emergence and kind of emergent complexity, but this idea that things are working towards a goal the way that any navigational system fundamentally does, is really not something that is very comfortable certainly for molecular biology …

— Michael Levin ( Developmental and synthetic biologist, Tufts University, USA)

All of us who study the origin of life find that the more we look into it, the more we feel it is too complex to have evolved anywhere. We all believe as an article of faith that life evolved from dead matter on this planet. It is just that life’s complexity is so great, it is hard for us to imagine that it did.

— Harold Urey ( Physical chemist, Nobel prize laureate, USA )

Origin of life is purely synthetic organic chemistry. There’s no way around it and I am perfectly situated to be commenting on this, to be critiquing the origin of life research. It is abiological, it is before biology takes over. This is purely synthetic organic chemistry and making these compounds it’s very simple four classes of compounds. You have to make them from what’s available on a presumed prebiotic earth and so the chemistry is not hard for synthetic organic chemists to follow …
Any trained synthetic organic chemist can follow me on this and I’ve never seen a synthetic organic chemist
disagree with me on this. In fact, the people that might disagree with me are biologists because they’ve never made anything.

Some might suggest that there are certain laws that we don’t yet know, undefined laws that would dictate the origin of first life. It’s very hard to comment on something that we don’t know anything about. However, one would have to have law upon law upon law upon law… One after another after another, to make the requisite molecules needed for life and then to have those requisite molecules assembled…
Because even if one had the molecules, which is very hard to do, how do you do the assembly?
We don’t know how to do that now…
If there’s some law to do this, remember just the interactome just the protein-protein interactions – within a single yeast cell the 3,000 proteins – it’s 10^79,000,000,000 on the possible combinations of just the interact on …
How do you get those to order? Of course, there is a large cascade of arrays that can get these to order but that always has life spawning life. We don’t dehydrate cells and get them to work together again …Cells will split and pass that information along to other cells. We don’t know how to spark these things and it can’t happen from a single unknown law…
You’d have to have unknown law upon unknown law upon unknown law …
Takes a lot of faith to do that. I’m not sure I have that level of faith, but if they do, good for them (for Darwinists)

— Professor James Tour (synthetic chemist / nanotechnologist, Rice University, Royal Society of Chemistry Centenary Prize winner )

Around 2007, I heard Dr Steven Benner (origin-of-life researcher) at JPL admit to a group of scientists and other employees that the problems in his field are so vexing, it was almost enough to make one become a creationist. The audience chuckled nervously. Such an admission must never be heard by the public. Benner listed problem after problem: chirality, genetic takeovers, accumulations of tar, and the difficulty of making ribose. When Benner is on camera, however, he smiles and talks about all the progress they’re making.

— David F. Coppedge, a former system administrator for the Cassini Mission to Saturn from 1997 to 2011, Jet Propulsion Laboratory ( JPL)

Prof. Lee Cronin: Origin of life research is a scam

the scam is if we just make this RNA, we’ve got this you know this uh this fluke event we know how that’s simple let’s make this phosphodiester or let’s make ATP or ADP we’ve got that part nailed let’s now make this other molecule another molecule and how many molecules are going to be enough ?

When you go back to Craig Venter, he invented his life form Cynthia … he made this wonderful cell and said – I invented life! – …. not quite … He facsimiled the genome from this entity (mycoplasma) …and made it in the lab – all the DNA … but he (Venter) didn’t make the cell – he had to take an existing cell and put in his genes … but it is remarkable, he couldn’t make the cell from scratchand even today, synthetic biologists can not make a cell from scratch … because there is some contingent information embodied outside the genome in the cell … and that is just incredible … so there is lots of layers to the scam” (an Youtube video auto-transcript)

— Prof. Lee Cronin ( synthetic chemist, origin-of-life researcher, University of Glasgow, UK )

The number of human interventions during origin-of-life experiments

Experimentalists in the field of prebiotic chemistry strive to re-enact what may have happened when life arose from inanimate material. How often human intervention was needed to obtain a specific result in their studies is worth reporting.

… I feel is it reasonable to report the number of manual interventions during an assay explicitly. This number can be quite high, as in the case of enzyme-free replication from activated nucleotides reported by us, where washing and deprotection steps were necessary to be able to measure the level of misincorporation of nucleotides mass spectrometrically5. It can also be high for multistep syntheses, mimicking entire biochemical pathways6,7. Understandably so, as self-organizing biochemical cycles are difficult to demonstrate experimentally8. Usually, one tries to keep the number of steps in the single digit range. When it becomes unavoidable to intervene as experimentalist, just state the number of discontinuities in the experimental conditions or human interventions!

Life is a non-equilibrium phenomenon. It requires an energy source that drives its reactions. Assuming that simple heating/cooling cycles could have driven the formation of functional biomacromolecules that were then able to harness the energy emitted by the sun via photosynthesis, seems unrealistic to me. Achieving the level of specificity required to successfully operate a protocell with genetic apparatus, metabolism, and cell division under strongly denaturing conditions is not easy, certainly when it comes to enzyme-free replication relying on the intrinsic specificity of small molecule interactions. So, the periodic addition of a chemical condensing agent may be unavoidable to drive biochemical reactions that are endergonic, even in “minimal intervention” experiments. Without the chemical activation, equilibrium (death) sets in. So, some level of human intervention may always be required for complex, multistep processes. After all, what the dominant activation agent was before enzymes began to use ATP will remain an enigma to many of us for the foreseeable future.

— Prof. Clemens Richert ( organic chemist, Universität Stuttgart, Germany )

More mainstream scientists’ critique of the origin-of-life research
(NATURE, FEB 26 2024)

Explaining isolated steps on the road from simple chemicals to complex living organisms is not enough …

Most scientists agree that these nanomachines are a product of selection — but selection for what, where and how?

There is no consensus about what to look for, or where …

Did life start on Earth in the hot waters of hydrothermal systems on land or in deep seas?

Combine that with the overarching importance of the question and it’s clear why the field is beset with over-claims and counter-claims, which in turn warp funding, attention and recognition

Strongly opposed viewpoints have coexisted for decades over basic questions …

For example, if life started in a warm pond on land, the succession of steps leading from prebiotic chemistry to cells with genes is surprisingly different from those that must be posited if the first cells emerged in deep-sea hydrothermal vents.

Building coherent frameworks — in which all the steps in the continuum fit together — is essential to making real progress.

It is too soon to aim for consensus or unity, and the question is too big; the field needs constructive disunity. Embracing multiple rigorous frameworks for the origin of life, as we advocate here, will promote objectivity, cooperation and falsifiability — good science — while still enabling researchers to focus on what they care most about. Without that, science loses its sparkle and creativity, never more important than here. With it, the field might one day get close to an answer.

— Nick Lane, PhD ( A biochemist, University College London, UK )
— Dr Joana Xavier, PhD (Chemical and Biological engineering, UK)

Nobel Laureate retracts non-reproducible Origin-of-life research paper

( A Nobel Laureate has retracted a 2016 paper in Nature Chemistry that explored the origins of life on earth, after discovering the main conclusions were not correct.  

Some researchers who study the origins of life on Earth have hypothesized that RNA evolved before DNA or proteins.  If true, RNA would have needed a way to replicate without enzymes. The Nature Chemistry paper found that a certain type of peptide — which may have existed in our early history — made it possible for RNA to copy itself. )

In retrospect, we were totally blinded by our belief [in our findings]…
We were not as careful or rigorous as we should have been (and as Tivoli was) in interpreting these experiments.

— Jack Szostak ( professor of chemistry, Nobel Laureate, Harvard University, USA )

Generalized self-driving is a hard problem, as it requires solving a large part of real-world AI. Didn’t expect it to be so hard, but the difficulty is obvious in retrospect.

— Elon Musk, chief engineer (SpaceX, Tesla)

Our finding casts serious doubts over literally thousands of studies that use phylogenetic trees of extant data to reconstruct the diversification history of taxa, especially for those taxa where fossils are rare, or that found correlations between environmental factors such as changing global temperatures and species extinction rates
… the results do not invalidate the theory of evolution itself. They do, however, put constraints on what type of information can be extracted from genetic data to reconstruct evolution’s path.

— Stilianos Louca, Department of Biology (University of Oregon)

I have been working with these traditional types of models for a decade now… I am one of the lead developers of a popular software package for estimating diversification rates from phylogenetic trees. And, as such, I thought I had a really good sense of how these models worked. I was wrong …

— Matthew W. Pennell (Biodiversity Research Centre, University of British Columbia)

Mutations are usually thought to be so rare, that when we see the same mutation in different individuals, the assumption is that those individuals shared an ancestor who passed the mutation to them both… But it’s possible that the mutation rate is so high in some of these non-B DNA regions that the same mutation could occur independently in several different individuals. If this is true, it would change how we think about evolution.

— Kateryna D Makova, biologist (Pennsylvania State University)

We have no idea how the molecules that compose living systems could have been devised such that they would work in concert to fulfill biology’s functions. We have no idea how the basic set of molecules, carbohydrates, nucleic acids, lipids and proteins were made and how they could have coupled in proper sequences, and then transformed into the ordered assemblies until there was the construction of a complex biological system, and eventually to that first cell. Nobody has any idea on how this was done when using our commonly understood mechanisms of chemical science. Those that say that they understand are generally wholly uninformed regarding chemical synthesis. Those that say, “Oh this is well worked out,” they know nothing—nothing—about chemical synthesis—nothing. … From a synthetic chemical perspective, neither I nor any of my colleagues can fathom a prebiotic molecular route to construction of a complex system. We cannot even figure out the prebiotic routes to the basic building blocks of life: carbohydrates, nucleic acids, lipids, and proteins. Chemists are collectively bewildered. Hence I say that no chemist understands prebiotic synthesis of the requisite building blocks, let alone assembly into a complex system. That’s how clueless we are. I have asked all of my colleagues—National Academy members, Nobel Prize winners—I sit with them in offices. Nobody understands this. So if your professors say it’s all worked out, if your teachers say it’s all worked out, they don’t know what they’re talking about…

— Professor James Tour (synthetic chemist / nanotechnologist, Rice University, Royal Society of Chemistry Centenary Prize winner )

Insects origin mystery

There’s been quite a bit of mystery around how insects first arose, because for many millions of years you had nothing, and then just all of a sudden an explosion of insects … The rocks could have contained insect fossils. The fact that they don’t indicates the dearth of insects during this period is real and not just an artifact of bad luck with preservation …

— Sandra Schachat, a graduate student at Stanford’s School of Earth, Energy & Environmental Sciences (Stanford Earth)

Dinosaurs origin remains a mystery

For over 170 million years they dominated the land, from small creatures just a few feet long to some of the largest animals ever to have walked Earth. But despite their long evolutionary history, the origin of dinosaurs remains shrouded in mystery… The earliest definitive dinosaur is not one animal but an entire ecosystem containing a few different species. There’s no universally accepted dinosaur species that lived earlier in time.

— Josh Davis, Digital News Editor for Natural History Museum London UK

There is no dispute between me and Richard Dawkins and there never has been, because he’s a journalist, and journalists are people that report what the scientists have found and the arguments I’ve had have actually been with scientists doing research

— E.O. Wilson, biologist, Harvard (called the Darwin of the 20th century )

Do cells use passwords in cell-state transitions? Is cell signaling sometimes encrypted?

Organisms must maintain proper regulation including defense and healing. Life-threatening problems may be caused by pathogens or by a multicellular organism’s own cells through cancer or autoimmune disorders. Life evolved solutions to these problems that can be conceptualized through the lens of information security, which is a well-developed field in computer science. Here I argue that taking an information security view of cells is not merely semantics, but useful to explain features of signaling, regulation, and defense. An information security perspective also offers a conduit for cross-fertilization of advanced ideas from computer science and the potential for biology to inform computer science. First, I consider whether cells use passwords, i.e., initiation sequences that are required for subsequent signals to have effects, by analyzing the concept of pioneer transcription factors in chromatin regulation and cellular reprogramming. Second, I consider whether cells may encrypt signal transduction cascades. Encryption could benefit cells by making it more difficult for pathogens or oncogenes to hijack cell networks. By using numerous molecules, cells may gain a security advantage in particular against viruses, whose genome sizes are typically under selection pressure. I provide a simple conceptual argument for how cells may perform encryption through posttranslational modifications, complex formation, and chromatin accessibility. I invoke information theory to provide a criterion of an entropy spike to assess whether a signaling cascade has encryption-like features. I discuss how the frequently invoked concept of context dependency may oversimplify more advanced features of cell signaling networks, such as encryption. Therefore, by considering that biochemical networks may be even more complex than commonly realized we may be better able to understand defenses against pathogens and pathologies.
— Alex Root, molecular biologist ( Memorial Sloan Kettering Cancer Center, New York, NY, USA )

Evolution is slow and gradual except when it is fast. It is dynamic and creates huge changes over time, except when it keeps everything the same for millions of years. It explains both extreme complexity and elegant simplicity. It tells us how birds learned to fly and how some lost that ability. Evolution made cheetahs fast and turtles slow. Some creatures are made big and others small, some gloriously beautiful and some boringly gray. It forced fish to walk and walking animals to return to the sea. It diverges except when it converges. It produces exquisitely fine-tuned designs except when it produces junk. Evolution is random and without direction except when it moves toward a target. Life under evolution is a cruel battlefield, except when it demonstrates altruism. Evolution explains virtues and vice, love and hate, religion and atheism and it does all this with a growing number of ancillary hypotheses…It explains everything without explaining anything well.

— Matti Leisola, bioengineer (former Dean of Chemistry and Material Sciences at Helsinki University of Technology)

Mutation protection paradox

Unbounded random change of nucleotide codes through the accumulation of irreparable, advantageous, code-expanding, inheritable mutations at the level of individual nucleotides, as proposed by evolutionary theory, requires the mutation protection at the level of the individual nucleotides and at the higher levels of the code to be switched off or at least to dysfunction. Dysfunctioning mutation protection, however, is the origin of cancer and hereditary diseases, which reduce the capacity to live and to reproduce. Our mutation protection perspective of the evolutionary dynamics of digital and nucleotide codes thus reveals the presence of a paradox in evolutionary theory between the necessity and the disadvantage of dysfunctioning mutation protection. This mutation protection paradox, which is closely related with the paradox between evolvability and mutational robustness, needs further investigation.

— William DeJong (INI-Research, NL), Hans Degens (Institute for Biomedical Research, UK)

Viruses don’t have a structure derived from a common ancestor

Cells obtain membranes from other cells during cell division. According to this concept of ‘membrane heredity’, today’s cells have inherited membranes from the first cells that evolved, and provides evidence that cells are derived from a common ancestor. Viruses have no such inherited structure … In a phylogenetic tree, the characteristics of members of taxa are inherited from previous ancestors. Viruses cannot be included in the tree of life because they do not share characteristics with cells, and no single gene is shared by all viruses or viral lineages. While cellular life has a single, common origin, viruses are polyphyletic – they have many evolutionary origins.

— Vincent Racaniello, microbiologist, virologist ( Columbia University’s College of Physicians and Surgeons, US )

Animal DNA modifier captured from bacteria 60 million years ago

It is hard to imagine how a single, horizontally transferred gene would form a new regulatory system, because the existing regulatory systems are already very complicated …

It’s almost unbelievable, just try to picture, somewhere back in time, a piece of bacterial DNA happened to be fused to a piece of eukaryotic DNA. Both of them became joined in the rotifer’s genome and they formed a functional enzyme. That’s not so easy to do, even in the lab, and it happened naturally. And then this composite enzyme created this amazing regulatory system, and bdelloid rotifers were able to start using it to control all these jumping transposons. It’s like magic.

— Irina A. Yushenova, PhD., molecular biologist (University of Chicago, Marine Biological Laboratory, USA)

Some Problems in Proving the Existence of the Universal Common Ancestor of Life on Earth

Although overwhelming circumstantial evidence supports the existence of the universal common ancestor of all extant life on Earth, it is still an open question whether the universal common ancestor existed or not . Theobald (Nature 465, 219–222 (2010)) recently challenged this problem with a formal statistical test applied to aligned sequences of conservative proteins sampled from all domains of life and concluded that the universal common ancestor hypothesis holds. However, we point out that there is a fundamental flaw in Theobald’s method which used aligned sequences. We show that the alignment gives a strong bias for the common ancestor hypothesis, and we provide an example that Theobald’s method supports a common ancestor hypothesis for two apparently unrelated families of protein-encoding sequences (cytb and nd2 of mitochondria). This arouses suspicion about the effectiveness of the “formal” test.

— Masami Hasegawa ( Department of Statistical Modeling, Institute of Statistical Mathematics, Japan )

Most of evolutionary trees could be wrong

It turns out that we’ve got lots of our evolutionary trees wrong.
For over a hundred years, we’ve been classifying organisms according to how they look and are put together anatomically, but molecular data often tells us a rather different story.
Our study proves statistically that if you build an evolutionary tree of animals based on their molecular data, it often fits much better with their geographical distribution.

We already have lots of famous examples of convergent evolution, such as flight evolving separately in birds, bats and insects, or complex camera eyes evolving separately in squid and humans.
But now with molecular data, we can see that convergent (repeated) evolution happens all the time – things we thought were closely related often turn out to be far apart on the tree of life.
It means that convergent evolution has been fooling us – even the cleverest evolutionary biologists and anatomists – for over 100 years!

— Matthew A. Wills
( Milner Centre for Evolution, Department of Biology & Biochemistry, University of Bath, UK )

The idea that biogeography can reflect evolutionary history was a large part of what prompted Darwin to develop his theory of evolution through natural selection, so it’s pretty surprising that it hadn’t really been considered directly as a way of testing the accuracy of evolutionary trees in this way before now.
— Dr. Jack Oyston
( Milner Centre for Evolution, Department of Biology & Biochemistry, University of Bath, UK )

DNA knots, tangles and supercoiling problems

[DNA molecule and cell nucleus] According to the usual comparison, it’s as if you had to pack 39 km of extremely thin thread into a tennis ball. Moreover, this thread is divided into 46 pieces (individual chromosomes) averaging, in our tennis-ball analogy, over 0.8 km long. Can it be at all possible not only to pack the chromosomes into the nucleus, but also to keep them from becoming hopelessly entangled?

All we can say currently is that we know some of the players addressing the problem. For example, there are enzymes called “topoisomerases” whose task is to help manage the spatial organization of chromosomes. Demonstrating a spatial insight and dexterity that might amaze those of us who have struggled to sort out tangled masses of thread, these enzymes manage to make just the right local cuts to the strands in order to relieve strain, allow necessary movement of genes or regions of the chromosome, and prevent a hopeless mass of knots.
Some topoisomerases cut just one strand of the double helix, allow it to wind or unwind around the other strand, and then reconnect the severed ends. This alters the supercoiling of the DNA. Other topoisomerases cut both strands, pass a loop of the chromosome through the gap thus created, and then seal the gap again. (Imagine trying this with miles of string crammed into a tennis ball)

— Stephen L. Talbott (Evolution scientist, The Nature Institute, USA)

The most common analytical method within population genetics is deeply flawed

It is expected that this method will give correct results because it is so frequently used. But it is neither a guarantee of reliability nor produces statistically robust conclusions

— Dr. Eran Elhaik (Associate Professor in molecular cell biology, Lund University, Sweden)

Techniques that offer such flexibility encourage bad science and are particularly dangerous in a world where there is intense pressure to publish.  If a researcher runs PCA several times, the temptation will always be to select the output that makes the best story

— Prof. William Amos (University of Cambridge)

Big errors in mouse and human genome annotation

The genome annotation says that ‘this gene is located on a specific chromosome and starts in one place and ends in another …’

But Gemma noticed that the annotation was wrong, such
that the gene was actually shorter than the public annotation.
This meant that the part of the gene that was thought to control
protein synthesis really just controlled RNA synthesis.

This doesn’t typically happen in our field, where a new model is accepted,
then proven to not be what it had claimed to be. We call it paradigm unshifting …

There are big errors in the mouse genome annotation and in the human genome annotation … The main goal for us was to help other researchers know about these issues so that these problems don’t reoccur in the future …

— Dr. C. Joel McManus (Associate Professor of Biological Sciences, Mellon College of Science, USA)

Rotten Corpses mistaken for missing links

Many evolutionary scenarios and assumed missing links may just be artefacts of rotting corpses of animals with completely modern anatomy.

Mitochondria are not captive bacteria

Admittedly, it is a daunting task to both honor Lynn Sagan for the enormous influence that she exerted over half a century of research in molecular evolution, as well as to set out the evidence that the modern tree of life (ToL) does not support her model of endosymbiotic origins of eukaryote organelles. We try to resolve this conflict by suggesting that had she known what we know now, nearly fifty years later, we are confident that she would have agreed with us that her symbiotic model of eukaryogenesis was not relevant to modern organisms.

— Ajith Harish ( Department of Cell and Molecular Biology, Section of Structural and Molecular Biology, Uppsala University, Uppsala, Sweden )

Commonly accepted theory within evolutionary biology disproved

We chose a classic example of adaptation … We found that the accepted wisdom about the molecular causes of the flies’ evolution is simply wrong.

The Adh (alcohol dehydrogenase) story was accepted because the ecology, physiology, and the statistical signature of selection all pointed in the same direction … But three lines of circumstantial evidence don’t make an airtight case.

— Joseph Thornton, PhD (Professor of Ecology and Evolution, University of Chicago, USA)

A thought experiment to expose the [Darwinists’] trickery:

You’ve probably heard about the example of bat wings and bird wings as a paradigmatic showcase of convergent evolution. This is because both groups have transformed the tetrapod foreleg into wings, but are not closely related. Each is nested deeply within different non-volant tetrapod groups with normally developed legs, so that the wings cannot be interpreted as homologous and inherited from an assumed winged common ancestor. Now imagine the counterfactual case that the majority of evidence (e.g., from comparative morphology and phylogenomics) would rather suggest that birds and bats were closest relatives (so-called sister groups). Suddenly the assumed convergence would of course be interpreted as a shared derived character that was inherited from a winged bat+bird ancestor as a homology (synapomorphy). The differences between both wing constructions would be explained away as autapomorphic specializations from a common ground plan, and biologists would emphasize that birds don’t just have feathered wings, but that beneath the feathers you can find small wing membranes (so-called patagia) that would be considered as homologous to the wing membrane of bats. With the discovery of the membraneous scanosoriopterygid wings, evolutionists would have celebrated the discovery of a predicted transitional form that proves the reconstructed ground plan and provides an indisputable confirmation of the evolutionary scenario linking bats and birds. Only science deniers would doubt such an obvious established fact of evolution, right?

— Günter Bechly, PhD (Paleo-entomologist, Ex-curator for amber and fossil insects in the department of paleontology at the State Museum of Natural History in Stuttgart, Germany)

Humpback whales in Antarctica blew bubbles in the shape of a Fibonacci spiral

Puffer fish creates 3D art crop circles

Are these fishes dead ?