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How much genetic difference separates us from our closest relatives? The conventional wisdom about humans and our closest ape relatives (chimps and bonobos) is that we share 98% of our DNA. That’s a big similarity, and implies that if we lined up our genomes side by side, only about 2 out of 100 DNA bases would differ. This figure is often used to show that we have only a tiny genetic difference from our closest relatives. To quote W. S. Gilbert of Gilbert and Sullivan, “Darwinian man, though well-behaved, at best is only a monkey shaved.”  Well, the differences go farther than mere shaving.

The “98% similarity figure” is wrong. And it’s wrong for several reasons. First, most ape genomes (chimps, gorillas, orangs, etc.) have not been as thoroughly sequenced as was the human genome. A lot of the data that went into the 98% figure was missing.  Second, you can’t just compare genomes by lining them up and looking for differences in base pairs at similar sequences.

Why not? Because the notion of “similar sequences” is ambiguous and, sometimes, meaningless. Since we diverged from our ape ancestors, there have been a lot of changes in every species’ DNA that prohibit us from simply “lining up the genomes”.  Transposable elements have invaded some species but not others, bits of the DNA have been duplicated, so there are species that have sequences that are not homologous. Bits of the genome have been inverted (turned around and reinserted), causing big differences in sequence in previously similar sequences. Further, pieces of the DNA have been moved from one chromosome to another, so DNA sequences previously in the same place are now in another place, leading to a difference in total sequence.

All this leads to a substantially greater DNA divergence between humans and chimps than the 98% figure.  These extra genomic differences were sussed out by Yoo et al. in a Nature paper  from April of last year that you can read by clicking below (or find the pdf here).They did a much improved job in sequencing six of our ape relatives: the chimp (Pan troglodytes), bonobo (Pan paniscus), Western gorilla (Gorilla gorilla), Bornean orangutan (Pongo pygmaeus), Sumatran orangutan (Pongo abelii), and the siamang (Symphalangus syndactylus), an endangered species of gibbon from SE Asia.

First, the authors give a revised set of divergence times based on DNA differences between living species.  The human vs. chimp/bonobo species, for example, split from their common ancestor about 5.5-6.3 million years ago (mya), roughly in line with previous estimates. The divergence between humans and other African apes (gorillas) occurred between 10.6 and 10.9 mya, and that between humans and orangutans about 18.2-19.6 mya.

There is a ton of genomic information in the paper, including a lessening of the similarity between humans and chimps, but also specific information about what genes and regulatory bits of DNA differ among species. These differences suggest some some intriguing future research. I’ll mention just a couple, but will refer you instead to a long tweet below which shows why the human-chimp differences have increased. It’s an excellent tweet that you can read pretty quickly, though it doesn’t detail all the many differences that the researchers describe in the Nature paper, which is exhausting for those outside the field. There are also genes whose sequences changed very rapidly, suggesting that they were acted on by natural selection.

There are a gazillion sequence and structural differences revealed among the species, including 229 bits of ape DNA (all species) that have evolved rapidly and are thus candidates for natural selection. The paper also reveals parts of the DNA that have evolved especially rapidly in the human lineage since we split from chimps/bonobos. These regions are called HAQERS, and could be candidates for the Holy Grail of such work: seeing “what makes us human”. But that question is a bit misguided.

Nevertheless, the authors found one gene, ADCYAP1, that “is differentially regulated in speech circuits.” The implication is that the changes may have something to do with why humans are the only ape with syntactic spoken language, but that gene does a lot of other stuff, too, so I don’t take that implication seriously. The FOXP2 gene, which evolved rapidly in the modern human genome relative to other species, has mutations that impede people’s ability to speak, and I well remember when it was touted as “the language gene” that enabled humans to speak. But further research showed that the accelerated human evolution of the gene was an artifact, and that the normal function of the gene is manyfold, so nobody these days takes FOXP2 seriously as the “speech gene”. All claims should be regarded as caveat emptor.

There are also several genes that are not only unique to humans, but are “associated with human evolution of the frontal cortex”, suggesting these account for our big brains. The photo below comes from the tweet shown next, and its caption comes from that tweet. (The average chimp brain is about 400 g in mass—less than a third the mass of the human brain, which weighs in at 1300-1400 g in adults.)  Again, caveat emptor with regard to the two specified genes.

Figure 3. Radiograph illustrating cranial expansion in the human lineage, which is associated with increased neocortical growth – Chimpanzee skull (left), Modern Human skull (right).

Other genes that differ strongly among ape species involve those producing immunoglobulin, major histocompatibility products (MCH) and T-cell receptors, but especially immunoglobulin genes—involved in production of antibodies. Why have these evolved so rapidly within apes? Your guess is as good as mine, but suggests that reaction to antigens was an important element of ape evolution.

Here is the authors’ summary, and most of the paper will be of interest only to geneticists familiar with the argot (not necessarily me):

The complete sequencing of the ape genomes analysed in this study significantly refines previous analyses and provides a valuable resource for all future evolutionary comparisons. These include an improved and more nuanced understanding of species divergence, human-specific ancestral alleles, incomplete lineage sorting, gene annotation, repeat content, divergent regulatory DNA and complex genic regions as well as species-specific epigenetic differences involving methylation. These preliminary analyses revealed hundreds of new candidate genes and regions to account for phenotypic differences among the apes. For example, we observed an excess of HAQERS corresponding to bivalent promoters thought to contain gene-regulatory elements that exhibit precise spatiotemporal activity patterns in the context of development and environmental response99. Bivalent chromatin-state enrichments have not yet been observed in fast-evolving regions from other great apes, which may reflect limited cross-species transferability of epigenomic annotations from humans. The finding of a HAQER-enriched gene, ADCYAP1, that is differentially regulated in speech circuits and methylated in the layer 5 projection neurons that make the more specialized direct projections to brainstem motor neurons in humans shows the promise of T2T genomes to identify hard to sequence regions important for complex traits. Perhaps most notably, we provide an evolutionary framework for understanding the about 10–15% of highly divergent, previously inaccessible regions of ape genomes. In this regard, we highlight a few noteworthy findings.

The importance of the paper for now seems to be the presentation of the sequences and their differences rather than explaining the differences or their significance in ape adaptations—especially in humans—for studying adaptive hypotheses involves a lot of work for each single region that differs among species or evolved quickly. Nevertheless, useful questions have been raised—like why genes involved in the immune response changed so rapidly—that will be subject to future work.

I am not sure who runs the Origins Unveiled site dealing with evolutionary anthropology, but based on the clarity of the tweet below from that site (click on screenshot to see the tweet in situ), it deserves more followers. It’s only about a year old, which may explain the follower issue.

This tweet from September of this year explains why the 98% similarity between humans and chimps drops to 84.7% when you take translocations, inversion, duplications, insertions, and other genomic rearrangements into account. And these rearrangements are not necessarily trivial, for duplications can lead to divergent gene families, and insertions can act to regulate genes in a new way.

Again, click below and read; it’s short and lucid:

I’ve shown one figure from the tweet above: the brain differences. Below is another figure showing how the 99% similarity between humans and chimps has traditionally been calculated, requiring alignment of nearly identical but perhaps slightly different bits of DNA. All captions come from the tweet. This figure shows how they line up chimp and human sequences (you see the gross similarity), but also that here there’s been a single nucleotide substitution in one of the two lineages, rendering this sequence 92.3% similar. (This is a made-up sequence for purposes of illustration.)  When you did that with the whole genome comparison based on earlier data, you got about a 2% difference. The problem, as I said, is that we didn’t have great chimp (or any ape) sequences and there are parts that you simply couldn’t line up this way. And those parts, when compared among species, increase the genetic difference between us and our closest relatives.

Figure 1 — Simplified Mock Alignment Illustrating Nucleotide Sequence Similarity Between Chimpanzee and Human Genomes. Out of 13 positions, one substitution (single-nucleotide variant, circled in red) results in ~92.3% DNA similarity. This example demonstrates the methodology behind the misleading 98–99% human-chimpanzee DNA similarity figures.

Below is another figure showing how various rearrangements, insertions, deletions, and translocations reduce similarity, but I’ll show only four of the six parts of the figure, giving the captions for a-d. You can see how these changes make humans and chimps less genetically similar than previously thought (again, captions come from the tweet; click to enlarge).  These are also “mock alignments” meant for purposes of illustration, but they do show the kind of thing seen in the Yoo et al. paper:

Figure 2 — Simplified Mock Alignments Illustrating Structural Variation Between Chimpanzee and Human Genomes. Note: Structural variants are not taken into account when calculating the 98–99% Chimpanzee-Human DNA similarity figures.
( a) Insertions and deletions contributing to sequence divergence. Out of 34 positions, 3 indels (insertions circled in orange; deletions in yellow) result in ~91.2% DNA similarity. Note: These indels are relative, as without a suitable outgroup (i.e. gorilla), an insertion in one genome appears as a deletion in the other.
(b) Duplication contributing to sequence divergence. Out of 34 positions, a duplication of 12 bases (duplicated segment encircled in blue; original in purple) results in ~64.7% DNA similarity.
(c) Inversion contributing to sequence divergence. Out of 34 positions, an inversion of 11 bases (encircled in green) results in ~67.6% DNA similarity. Note: Although bases may match within the inverted region, they do not contribute to sequence similarity due to misalignment. Without a suitable outgroup (i.e. gorilla), it is unknown whether the inversion occurred on the chimpanzee or human genome.
(d) Translocation contributing to sequence divergence. Out of 34 positions, a translocation of 20 bases (encircled in brown) results in ~41.2% DNA similarity. Note: A translocation is a DNA segment that has been “copy and pasted” or “cut and pasted” from another part of the genome.

So, when you hear that we’re nearly genetically identical to our closest relatives, just say, “Wait a tick. Not all that identical.” We have about 15% difference in sequence, which is not trivial.

UPDATE: I’m aware now that creationists and IDers have been using this 85% to cast doubt on human evolution, our place in the ape family tree, and whether evolutionists are honest.  This is bogus: the 85% vs. 98% depends on two different methods of calculating similarity. Which ever method you choose (alignment vs. total genomic similarity), the same family tree of the great apes appears, with chimps/bonobos our closest ancestors, then gorillas a bit more distance, and then orangutans, and then other apes.  The point of this post is not to cast doubt on human or ape evolution, but to show different ways of calculating genetic similarity.

Today we have some marine mammal photos taken by Marcel van Oijen. Marcel’s captions are indented, and you can enlarge the photos by clicking on them.  Here’s a screenshot of the site, the island of Inchkeith:

Seal pup counting on the island of Inchkeith

Marcel van Oijen

The island of Inchkeith lies a few km from Scotland’s capital Edinburgh in the Firth of Forth, the sea-arm to the north. The last human to live on the island, the lighthouse-keeper, left in 1986. (The lighthouse is now controlled remotely from Edinburgh as are most lighthouses in Scotland.) Wildlife has since come back, and there is now a thriving colony of grey seals (Halichoerus grypus) producing around 900 pups each year. I took the photos below during the pup count of 29 November organised by the Forth Islands Heritage Group of volunteers.

This is near the harbour where we arrived, and we had to be careful not to get too close. Fortunately the female was busy keeping the male away from her pup. Cannibalism does happen occasionally.

Looking back to the harbour with the second group of volunteers just arriving. Note the many seals on the beach and in the water

Mating couple. The female life cycle is intense: a few weeks after giving birth and after the pup is weaned, they can be impregnated again:

This pup has moulted (i.e., lost its fluffy white baby-coat called the lanugo), so it will be three to four weeks old. At that age pups will be weaned and have to fend for themselves.

Two young pups who have just begun moulting, starting from the head:

Female seals carefully watching us:

This pup is nearly done moulting, some fluff left on top:

A moulted pup with an unusual colour, not the standard dappled grey:

Overview of ‘our’ patch of the island where we counted around 200 pups:

The most affectionate mother we saw on the island. She occasionally rolled on her back with eyes closed but always kept patting her pup with her front flipper:

Looking back to Inchkeith with fond memories!:

Knotted structures once imagined by Lord Kelvin may actually have shaped the universe’s earliest moments, according to new research showing how two powerful symmetries could have created stable “cosmic knots” after the Big Bang. These exotic objects may have briefly dominated the young cosmos, unraveled through quantum tunneling, and produced heavy right-handed neutrinos whose decays tipped the balance toward matter over antimatter.

Well, winter is still two weeks away, but tell that to the clouds.  Last night it snowed several inches in Chicago—and it’s still coming down. The streets seem impassable, putting the kibosh on my plans to do grocery shopping today, and I’m out of the essentials at work, including peanut butter and tuna.

But it’s still lovely. Here, for example, is Botany Pond. I hope the turtles are hibernating safely despite the pond’s gravel bottom.

My tracks on the way to work. Could you identify these as human tracks? It looks as if I was weaving drunkenly, but I was just avoiding certain spots.

But here are tracks of another creature. The quiz is, WHAT MADE THESE TRACKS?  Answer at 11 a.m. Chicago time.  Please don’t put your answers in the comments, but if you think you know, do say that.

And you’re lucky if you can get to the grocery store!

Scientists have discovered that moonquakes, not meteoroids, are responsible for shifting terrain near the Apollo 17 landing site. Their analysis points to a still-active fault that has been generating quakes for millions of years. While the danger to short missions is low, long-term lunar bases could face increasing risk. The findings urge future planners to avoid building near scarps and to prioritize new seismic instruments.

A severe accident at the Baikonur Cosmodrome involving a wrecked maintenance cabin has indefinitely delayed Russia's ability to launch crewed missions and payloads to the International Space Station (ISS).

For the past two weeks I have had bits of a song’s melody in my head, but I couldn’t remember any words, and that made it tough to remember.  Then, last night, I remembered a bit of one line, which, in my brain, went “Didn’t it seem right to walk along the beach last night”, but I still couldn’t find the song from Googling that, either. (It turns out that the word is “sand,” not “beach”.)  Amazingly, though, as soon as I remembered that line I remembered the end of the stanza as well its title “It could be we’re in love”.  Then I was able to find it by Googling.

It amazes me that my brain had been working unconscionsly on this thing for weeks, and finally the neurons came through for me.

The song is “It Could Be We’re in Love”, released in 1967 by The Cryan’ Shames, a Chicago group. It’s a good but not a fantastic song, but it’s catchy and somehow it was lingering in my brain and popped up for unknown reasons.  There are two versions, one with laughing in it and another with some psychedelic vibrato. I’ll put up both.

First, the better 1966 psychedelic version released on LP: (psychedelic vibrato at 1:41).

And here’s the laughing version, from the 1967 single (laughing at 1:49):

The Jesus and Mo artist sent this cartoon with the caption: “A Chrismassy Friday Flashbacck today, from 9 years ago.” Jesus is beefing about the nonexistent “war on Christmas” in the UK:

SQUIRE aims to detect exotic spin-dependent interactions using quantum sensors deployed in space, where speed and environmental conditions vastly improve sensitivity. Orbiting sensors tap into Earth’s enormous natural polarized spin source and benefit from low-noise periodic signal modulation. A robust prototype with advanced noise suppression and radiation-hardened engineering now meets the requirements for space operation. The long-term goal is a powerful space-ground network capable of exploring dark matter and other beyond-Standard-Model phenomena.

SQUIRE aims to detect exotic spin-dependent interactions using quantum sensors deployed in space, where speed and environmental conditions vastly improve sensitivity. Orbiting sensors tap into Earth’s enormous natural polarized spin source and benefit from low-noise periodic signal modulation. A robust prototype with advanced noise suppression and radiation-hardened engineering now meets the requirements for space operation. The long-term goal is a powerful space-ground network capable of exploring dark matter and other beyond-Standard-Model phenomena.

New findings challenge the widespread belief that AI is an environmental villain. By analyzing U.S. economic data and AI usage across industries, researchers discovered that AI’s energy consumption—while significant locally—barely registers at national or global scales. Even more surprising, AI could help accelerate green technologies rather than hinder them.

News Items: Cognitive Legos, China's Planting Lots of Trees, Misinformation and Birth Control, Dark Matter Detection, Asteroid Bennu Ingredients for Life; Who's That Noisy; Your Questions and E-mails: Climate Denial, Calcium Cardiac Scans; Science or Fiction

What is “gum”? Most people have probably never considered this question, and might answer something like a chewy material you can put in your mouth. But, to a scientist they might answer something like “nitrogen-rich polymeric sheets”, because precisely defining the chemistry of a material is important to them. Or at least, that’s what they called a type of organic material found in the sample collected of the asteroid Bennu by the OSIRIS-REx spacecraft. But more informally, scientists have taken to calling it “space gum”, and the process it formed under is making some of them question current models of asteroid formation.

SPHERE’s detailed images of dusty rings around young stars offer a rare glimpse into the hidden machinery of planet formation. These bright arcs and faint clouds reveal where tiny planet-building bodies collide, break apart, and reshape their systems. Some disks contain sharp edges or unusual patterns that hint at massive planets still waiting to be seen, while others resemble early versions of our own asteroid belt or Kuiper belt. Together, the images form one of the most complete views yet of how newborn solar systems evolve and where undiscovered worlds may be hiding.

Scientists have discovered how to electrically power insulating nanoparticles using organic molecules that act like tiny antennas. These hybrids generate extremely pure near-infrared light, ideal for medical diagnostics and advanced communications. The approach works at low voltages and surpasses competing technologies in spectral precision. Early results suggest huge potential for future optoelectronic devices.

Scientists have discovered how to electrically power insulating nanoparticles using organic molecules that act like tiny antennas. These hybrids generate extremely pure near-infrared light, ideal for medical diagnostics and advanced communications. The approach works at low voltages and surpasses competing technologies in spectral precision. Early results suggest huge potential for future optoelectronic devices.

Hot exozodiacal dust can thwart our efforts to detect exoplanets. It causes what's called coronagraphic leakage, which confuses the light signals from distant stars. The Habitable Worlds Observatory will face this obstacle, and new research sheds light on the problem.

A video that appeared on CGTN's Hot Take details four missions that China will be sending to space in the coming years, including a survey telescope that will search for Earth 2.0.

A powerful geomagnetic superstorm is a once a generation event, happening once every 20-25 years. Such an event transpired on the night of May 10/11, 2024, when an intense solar storm slammed into the Earth’s protective magnetic sheath. Now, a recent study shows just how intrusive that storm was, and how long it took for the Earth’s plasma layer took to recover.

Observations with the SPHERE instrument on the European Southern Observatory's VLT revealed the presence of debris rings similar to structures in our Solar System. SPHERE found rings similar to the Kuiper Belt and the Main Asteroid Belt. Though individual asteroids and comets can't be imaged, these debris rings infer that other solar systems have architectures similar to ours.