Evolution and a Gene Expression Code Library 0 (0)

Isabel Almudi's photo: mayflies, one of the 20 species studied in Federica Mantica et al.'s paper.Scientists have found gene groups we have in common with nearly all animals: thousands of them, from a code library that’s more than half a billion years old.

I’ll be talking about that this week, plus why I see no problem with studying this vast and ancient universe.


Still Learning Life’s Long Story

Illustration from 'Discovery of the oldest bilaterian from the Ediacaran of South Australia': 'Reconstruction of Ikaria in life position forming a Helminthoidichnites-type trail' (received for review January 21, 2020; approved February 17, 2020; published March 23, 2020)
Helminthoidichnites-type trail left by Ikaria. Illustration from “…oldest bilaterian…”. (2020)

We’ve learned a great deal about life’s long story since my youth.

Back then, scientists didn’t know why a whole bunch of complex critters suddenly showed up in the fossil record, starting about 539,000,000 years back.

The “Cambrian explosion” is still something of a mystery, and may not have been particularly ‘explosive’. It could be just where the known fossil record picks up after the “Avalon explosion”, some 575,000,000 years ago.

Unless both explosions aren’t so much sudden bursts of diversity, as cases where we’ve got lots of fossils from two eras, but not so many from others.

The point I’m groping for is that we’re learning a lot about life’s long story — and Earth’s, and ours — and it looks like we have a great deal left to learn.

Kevin A. Simonin, Adam B. Roddy: Genome size in 393 land plant species. (2018)My high school science textbooks didn’t use terms like bilaterians and genome evolution: maybe because ‘most animals have bilateral symmetry’ and ‘some animals have radial symmetry’ fit the lesson plan better, and that’s another topic.

At any rate, genome evolution wasn’t mentioned at all, since that particular subject didn’t exist until the 1970s. I’m putting links to a mess of ‘what is this’ resources in the footnotes, and will explain why science and using our brains doesn’t bother me — later.

Now, before getting to how we share genes with fruit flies, a few definitions.

Bilaterians are critters with a distinct right and left side, top and bottom, front and back. Pretty much all animals these days are bilaterians. Even echinoderms, as larvae, are bilaterally symmetrical before they develop their adult five-fold radial symmetry.1

Bilateral Symmetry and Oh, Look! It’s a — Thing

Photo from Verisimilus: Cast of Dickinsonia costata from Australia, an organism in the Ediacaran biota, possibly an animal.Being bilateral started early — with critters like Dickinsonia, a might-be-an-animal that hasn’t been around for the last 550,000,000 years. Or disappeared from the fossil record then, at any rate.

Then again, maybe Dickinsonia wasn’t bilaterally symmetrical. Some researchers say the might-be-an-animal had glide reflection symmetry, which looks like bilateral symmetry but isn’t.

Maybe someday I’ll talk about “…a geometric transformation that consists of a reflection across a hyperplane and a translation (‘glide’) in a direction parallel to that hyperplane, combined into a single transformation….”

But not today. I’m still recuperating, and will be doing well to get this thing ready in time.

Next, before getting to a recent analysis of animal genomes, a (very) little about how we know what we know about critters that aren’t around any more.

Sometimes we find fossils of critters with tracks they left just before dying. Often we don’t. The good news is that we can infer a great deal about how a critter acted from the traces/tracks it left. And that’s yet another topic.

Studying critters like Dickinsonia would be a lot easier, if we could observe living individuals: or even had access to specimens preserved with formaldehyde and alcohol. But those aren’t options creatures that have been dead since long before the non-avian dinosaurs died.

The good news is that scientists have been learning a great deal about how biochemicals work, and how they’ve been changing.

That, along with mathematical tools I hadn’t known about before I started re-learning how we’re studying our past, let scientists make pretty good estimates how life worked at the sub-cellular level in ages long past.

And, which is what I’m talking about this week, when assorted genes have changed.2


Bilaterians: 700,000,000 Years of Building on the Basics

Isabel Almudi's photo: mayflies, one of the 20 species studied in Federica Mantica et al.'s paper.
“The mayfly, one of the 20 species studied in the paper.” (CRG) Photo: Isabel Almudi

Evolution’s recipe book: How ‘copy paste’ errors led to insect flight, octopus camouflage and human cognition
Center for Genomic Regulation, Phys.org (April 15, 2024)

“Seven hundred million years ago, a remarkable creature emerged for the first time. Though it may not have been much to look at by today’s standards, the animal had a front and a back, a top and a bottom. This was a groundbreaking adaptation at the time, and one which laid down the basic body plan which most complex animals, including humans, would eventually inherit.

‘The inconspicuous animal resided in the ancient seas of Earth, likely crawling along the seafloor. This was the last common ancestor of bilaterians, a vast supergroup of animals including vertebrates (fish, amphibians, reptiles, birds, and mammals), and invertebrates (insects, arthropods, mollusks, worms, echinoderms and many more).

“To this day, more than 7,000 groups of genes can be traced back to the last common ancestor of bilaterians, according to a study of 20 different bilaterian species including humans, sharks, mayflies, centipedes and octopuses….”

The CRG research team published their research in the April 15, 2024 Nature Ecology & Evolution, an online-only monthly peer-reviewed scientific journal.

I didn’t find the April 15, 2024 paper: either because I don’t have the right credentials, or maybe I wasn’t looking in the right place. I did, however, find a prepress draft: which I’ll assume isn’t all that different from the final version.

CRG stands for Center for Genomic Regulation — and Centre de Regulació Genòmica.

It’s one of those happy — or confusing — situations where an an outfit’s name in its own language yields an acronym that’s similar to the acronym it’d have in my language. In this case, it’s Center for Genomic Regulation.

What they regulate, and why, is something I haven’t discovered. I did, however, find their ‘what we do’ page: the English-language version.

CRG (Centre de Regulació Genòmica (Catalan)): “General information
(Center for Genomic Regulation (English))

“…The mission of the CRG is to discover and advance knowledge for the benefit of society, public health and economic prosperity.

“The CRG believes that the medicine of the future depends on the groundbreaking science of today. This requires an interdisciplinary scientific team focused on understanding the complexity of life from the genome to the cell to a whole organism and its interaction with the environment, offering an integrated view of genetic diseases….”

Regulació apparently translates into English as “regulation”, with pretty much the same meaning for both.

  • regulation: “an official rule or the act of controlling something”
    (Cambridge English Dictionary)
  • Regulació: regulation: “an official rule that controls how something is done”
    (reglament, norma)
    (Cambridge English-Catalan Dictionary)

I’m guessing that one the CRG’s functions is regulating how their researchers study “the complexity of life from the genome to the cell…” — which strikes me as a good idea.

Studying this wonder-packed universe, and our place in it, is a good idea. So is remembering that ethics matter.3 (Catechism of the Catholic Church, 2258, 2292-2295)

Ancient Genes, Rewritten

Figure 1: Dataset overview and global patterns of gene expression across bilaterian tissues. a. RNA-seq dataset overview. Left: phylogenetic tree including the common names and scientific acronyms of the 20 bilaterian species considered in this study. Evolutionary distances were derived from 81 (MYA: million years ago) and animal silhouettes downloaded from http://phylopic.org/ (see Acknowledgements for credits to Phylopic icons). Center: scheme of RNA-seq meta-samples. The number of meta-samples for each species (rows) and tissue (columns) is reported. .... Right: barplot with the total number of processed RNA sequencing (RNA-seq) samples per species. b. Coordinates of the first (PC1; x axis) and second (PC2; y axis) principal components from a principal component analysis (PCA) performed on the best-ancestral orthogroups normalized expression matrix....
caption

Evolution of tissue-specific expression of ancestral genes across vertebrates and insects
Federica Mantica, Luis P. Iñiguez, Yamile Marquez, Jon Permanyer, fAntonio Torres-Mendez, Josefa Cruz, Xavi Franch-Marro, Frank Tulenko, Demian Burguera, Stephanie Bertrand, Toby Doyle, Marcela Nouzova, Peter Currie, Fernando G. Noriega, Hector Escriva, Maria Ina Arnone, Caroline B Albertin, Karl R Wotton, Isabel Almudi, David Martin, Manuel Irimia; bioXriv, the preprint server for biology (Posted December 21, 2023)

“…How did this ancient organism specify such a great variety of biological structures? Since all its cells shared the same genome, gene expression regulation was likely key for the generation of unique transcriptomes across these ancestral tissue types, and consequently for the emergence of their distinctive biological functions.

“The bilaterian ancestor gave rise to the vast majority of extant animals, where the original body plan and tissues have been greatly diversified and modified. Determinants of animal evolution include changes in gene complements (i.e. gene gains/losses and gene duplications), divergence of protein-coding sequences 4-6 and regulatory changes in gene expression….”

There’s a whole lot going on here, but this week I’ll focus on an unexpected detail.

Normally, I’d have gone off on several tangents at this point. But CRG’s piece on Phys.org sums up most of what I’d have said.4

“…To this day, more than 7,000 groups of genes can be traced back to the last common ancestor of bilaterians, according to a study of 20 different bilaterian species including humans, sharks, mayflies, centipedes and octopuses. The findings were made by researchers at the Centre for Genomic Regulation (CRG) in Barcelona and are published today in the journal Nature Ecology & Evolution.

“Remarkably, the study found that around half of these ancestral genes have since been repurposed by animals for use in specific parts of the body, particularly in the brain and reproductive tissues. The findings are surprising because ancient, conserved genes usually have fundamental, important jobs that are needed in many parts of the body….”
(“Evolution’s recipe book: How ‘copy paste’ errors led to insect flight, octopus camouflage and human cognition“, Center for Genomic Regulation, Phys.org (April 15, 2024)) [emphasis mine]

Gene Duplication: Let the Modding Begin!

Figure. 4: Tissue-specificity gains are associated with gene duplication and specialization. a. Total numbers of tissue-specificity gains and losses across all nodes and species. b. Relative proportions of tissue-specificity gains and losses across tissues within each node and species. Full/transparent shades of tissue colors represent gains/losses, respectively. c. Total number of tissue-specificity gains across nodes on each phylogenetic branch. ... Abbreviations: N: neural, T: testis, O: ovary, M: muscle, X: excretory, E: epidermis, D: digestive, A: adipose, Euarch: Euarchontoglires. Cycl: Cyclorrapha. Deut: Deuterostoma. Prot: Protostoma.
caption

Recapping, we share thousands of gene groups with pretty much all other animals. And a great many of those genes are repurposed from genetic code that’s very probably needed for basic biological functions.

But bilaterians stay alive: because — apparently — very early on, these ‘need these for basic functions’ genes got duplicated.

With the original genes in place and doing their jobs, bilaterians now had a sort of code library available for experiments. Which eventually, after a great deal of modding, led to centipedes, mosquitoes, zebrafish, and us.

And yes, I’m anthropomorphizing a natural process.5 Maybe more than just one.

That’s another tangent I don’t have time — or energy — for this week.

Instead, I’ll talk about why I’m not offended that we share genes with zebrafish, sea urchins, and centipedes. And why I see no problem in taking both faith and reason, science and religion, seriously.


Faith and Reason, Science and Religion

Detail, Gentile da Fabriano's 'Valle Romita Polyptych.' (ca. 1411)I don’t see natural processes as threats to my faith, partly because I think St. Thomas Aquinas is right. Secondary causes are real.

He talked about that sort of thing, at length:

“…God’s immediate provision over everything does not exclude the action of secondary causes; which are the executors of His order, as was said above (Question [19], Articles 5, 8)….”
(First Part, Question 22, Article 3)
“…For the providence of God produces effects through the operation of secondary causes, as was above shown (Question [22], Article 5)….”
(First Part, Question 23, Article 5)
“…The fact that secondary causes are ordered to determinate effects is due to God; wherefore since God ordains other causes to certain effects He can also produce certain effects by Himself without any other cause….”
(First Part, Question 105, Article 1)
“…God fixed a certain order in things in such a way that at the same time He reserved to Himself whatever he intended to do otherwise than by a particular cause. So when He acts outside this order, He does not change….”
(First Part, Question 105, Article 6)
(“Summa Theologica“, Thomas Aquinas (ca. 1265-1274))

Briefly, I think God creates everything. I’d better, if I’m going to be a Catholic. (Genesis 1:1-2:3, 2:4-25; Catechism, 279-314)

And I think that “everything” includes natural processes we call physical laws. Like Newton’s laws of motion.6

We’ve known about secondary causes for three quarters of a millennium. Longer, but that’s yet again another topic for another time.

“Truth Cannot Contradict Truth”

USGS/Graham and Newman's geological time spiral: 'A path to the past.' (2008)So how come some folks seem convinced that they must either believe that “God produces effects through the operation of secondary causes” and sometimes “acts outside this order”, or that because natural processes are knowable and predictable, God doesn’t exist?

I don’t think you’ll ever hear someone put the ‘science disproves God’ or ‘God forbids science’ attitude that way. But I keep running into variations on the theme.

Because I’m a Catholic, and know a little about my faith, I see no problem with being interested in God’s creation. Unless I put that interest ahead of God in my priorities.

Putting anything — science, politics, canasta, whatever — where God belongs would be idolatry, and a very bad idea. (Catechism, 2112-2114)

But studying God’s creation? Provided we don’t go nuts about it, that’s a good idea.

If we keep learning, we’ll discover that scientific truths we’re uncovering and truths of faith harmonize. We’ll learn more about God, while developing greater admiration for God and God’s work. Faith and reason, science and religion, get along. Or should. (Catechism, 31-32, 35-36, 159, 274, 283, 319, 341, 1704)

Granted, now and again we learn something that upsets preconceived notions. But if we keep collecting data and thinking: we’ll learn that what’s true is still true.

“…if methodical investigation within every branch of learning is carried out in a genuinely scientific manner and in accord with moral norms, it never truly conflicts with faith, for earthly matters and the concerns of faith derive from the same God. … we cannot but deplore certain habits of mind, which are sometimes found too among Christians, which do not sufficiently attend to the rightful independence of science and which, from the arguments and controversies they spark, lead many minds to conclude that faith and science are mutually opposed.…”
(“Gaudium et Spes“, Pope St. Paul VI (December 7, 1965)) [emphasis mine]

“…God, the Creator and Ruler of all things, is also the Author of the Scriptures — and that therefore nothing can be proved either by physical science or archaeology which can really contradict the Scriptures. … Even if the difficulty is after all not cleared up and the discrepancy seems to remain, the contest must not be abandoned; truth cannot contradict truth….”
(“Providentissimus Deus“, Pope Leo XIII (November 18, 1893) [emphasis mine]

Four Centuries in Europe: the Black Death, Wars, and a Label

Propaganda print, celebrating faith-based vandalism: illustrating Catholic worship of the seven-headed Beast, a devil with a crucifix, and righteous people smashing statues. (1566) from Rijksmuseum, via Wikimedia Commons, used w/o permission
Smashing statues in northern Europe. (1566)

I don’t know why Newton's second law of motion, in modern notation. F = dp/dt isn’t used as (alleged) proof that God doesn’t exist, and that’s still another topic. Topics.

In any case, although physics isn’t shunned, denouncing evolution became an important part of one-hundred-percent-real-American Christianity.

I strongly suspect that the ‘evolution, or God, but not both’ attitude has roots in 19th century English politics.

And that mess oozed out of what many folks call Europe’s religious wars.

'Pontis Antwerpiani fractura' illustration from Famiano Strada's book (possibly 'De bello Belgico decas secunda'). (1647)) via Wikimedia Commons, used w/o permissionThe label’s not entirely without merit.

But I see conflicts like the Hundred Years War (14th-15th century), Dutch-Portuguese War (16th-17th century), and Thirty Years War (17th century), more as turf wars.

That may take explaining.

I’m covering several centuries of human folly in a few paragraphs, so bear in mind that this is an extreme oversimplification.

When folks started re-establishing inter-regional trade routes, Europe’s southern princes got first crack at these economic opportunities. Or, rather, southern merchants did, and I’m wandering off-topic again.

They were also first in line for the Black Death (14th century). But that didn’t last, and when the plague ended they were still first in line for imports and exports.

Europe’s northern princes were profiting from inter-regional trade, too; but they arguably felt that they were getting hand-me-downs from the comparatively wealthy south.

It didn’t help that at this point, the Catholic Church was the only pan-European authority, and the largest single European landholder.

I see that situation more as a post-Roman reflection of ancient religion-state relationships, than as a Catholic plot. Good grief, I’m wandering again.

By the 16th century, the Catholic Church was due for an overhaul. We hit these rough patches every half-millennium or so, but this one boiled over into a mess we’re still cleaning up.7

A King, the Age of Enlightenment, and a Few Good Ideas

Anicet Charles Gabriel Lemonnier's 'Reading of Voltaire's L'Orphelin de la Chine' (a tragedy about Ghengis Khan and his sons, published in 1755), in the salon of Madame Geoffrin (Malmaison, 1812).
Enlightenment-era folks reading Voltaire in Madame Geoffrin’s salon, as imagined by Lemonnier. (1812))

Holbein's Henry VIII, king of England and mini-pope. (1542)Long story short, England’s Henry VIII decided that he’d set up his own personal church, with himself as a mini-pope.

His Church of England was a smashing success, and arguably provided a model for other national leaders who felt inhibited by their political connections with the Church.

Recapping:

  • Black Death (14th century)
  • Hundred Years’ War (14th-15th century)
  • Dutch-Portuguese War (16th-17th century)
  • Thirty Years’ War (17th century)

England’s Henry VIII was an early 16th century king. His Church of England is still a going concern, and Antidisestablishmentarianism is — a rabbit hole for another day.

Meanwhile, folks who weren’t cooking up religion-themed propaganda for this, that, or the other king, duke, marquess, or whatever, were — — —

Actually, I figure a great many folks were simply living their lives and hoping the powers that be would let them do so.

But a fair number of non-noble aristocrats were getting thoroughly fed up with Europe’s near-constant slaughters.

Many of these folks somehow twigged to the illogic of one king’s subjects killing another king’s subjects. And both butcher brigades shouting with apparent sincerity that God was backing their boss.

That, and aristocrats thinking about what we’d eventually call the Scientific Revolution, gave us the Age of Enlightenment.

An artist's impression of the 'Fête de la Raison/Festival of Reason' at Notre Dame, Paris, during the French Revolution. (1793) From Bibliothèque nationale de France, via Wikimedia Commons, used w/o permission.The Age of Enlightenment didn’t light the Beacon of Reason, driving the Shadows of Superstition, Ignorance and Religion into the Abyss prepared for them.

But it did, I think, help put some good ideas into the mix: like the still-slightly-suspected notion that thinking is a good idea, and that folks who aren’t in charge matter anyway.

I don’t know who, how, and where “Age of Enlightenment” got traction as a label for that particular period.8

English Politics and All-too-Familiar Attitudes

'Man is but a Worm' cartoon, caricaturing Darwin's theory, from the Punch almanac for 1882. (1981)Here’s where I finally get around to English politics and 19th century weirdness that we’re still dealing with.

Darwin’s theory of evolution got mixed up in 19th century English politics.

Inheritors of Henry VIII’s Church of England had, among other things, a tight hold on England’s educational system.

The C. of E. set also attacked ideas they hadn’t invented: which I see as part of general human foolishness.

On the other hand, liberal Anglicans attacked the establishment’s position, and folks like Thomas Huxley defended Darwin’s theory — in part, maybe — because it helped pry England’s schools out of the religious establishment’s grip.

He might have defended Darwin’s theory anyway. But his politics probably encouraged greater enthusiasm.

I’m oversimplifying things a lot, but I think you get the idea.

These attacks on the status quo wouldn’t have endeared science to Englishmen who liked their nation’s official church and school just the way they were.

Maybe old-school English views of evolution encouraged old-school Americans to see the newfangled idea as a threat. I don’t know.

Preferring the status quo isn’t limited to Brits. To this day, some Americans have trouble dealing with an increasingly non-English America. Back in the 19th century, the ‘being American is being English’ attitude probably had wider appeal.

At any rate, time passed. Scientists kept studying reality, while some other folks kept trying to ignore newfangled ideas.

Someone founded the Anti-Evolution League of Minnesota. That grew into the Anti-Evolution League of America, with headquarters in Kentucky. Tennessee’s legislature defended traditional values — their version — with the 1925 Butler Act.

That led to the Scopes Monkey Trial:9 which helped maintain the notion that someone could either accept God’s universe as-is, or stalwartly ignore what we’re learning.

Using my Brain, Admiring God’s Universe

Wiley Miller's Non Sequitur: The Church of Danae vs. logic and the laws of physics. (August 24, 2016) used w/o permission.I’ve talked about evolution, science, history, and politics: but how do I feel about living in a universe that doesn’t work quite the way my ancestors thought it did?

Pretty good, actually. Which in this case makes accepting the truths we’re uncovering exciting, rather than upsetting or disturbing.

But, whether I’m feeling good or otherwise, using my brain — thinking — is important.

Again, that’s because I’m a Catholic.

I’m human, so I think I’m “an animal endowed with reason”. (Catechism, 1951)

I also experience emotions. They’re part of being human. By themselves, emotions aren’t good or bad. They’re just there. What I decide to do about my feelings: that’s where good and bad come in. (Catechism, 1762-1770)

I’m “an animal endowed with reason”, but I don’t have to think.

I have free will, so using my brain is a choice, not a hardwired response. It’s also a good idea. (Catechism, 1730, 1778, 1804, 1951, 2339)

About thinking or ‘trusting my feelings’: I was born during the Truman administration, am a very emotional man, and have learned that using my feelings as a guide can be highly imprudent.

A few more points, and I’m done.

Besides being “an animal endowed with reason”, I think each of us is made “in the image of God”, with body AND soul. (Catechism, 355-373)

We’ve known for millennia that we’re made from the stuff of this world.

“then the LORD God formed the man out of the dust of the ground and blew into his nostrils the breath of life, and the man became a living being.”
(Genesis 2:7)

All that’s changed recently is how much we know about “the dust of the ground” God uses: and getting upset about the Almighty’s design aesthetic doesn’t make sense. Not to me.

Last point: each time we learn something new about God’s universe, it’s an opportunity for praise and and admiration.

“…These discoveries invite us to even greater admiration for the greatness of the Creator….”
(Catechism of the Catholic Church, 283)

I’ve talked about this before:


1 Symmetry, sea urchins, and life’s early years:

2 How we know what we know, in part:

3 Genetics, language, bioethics, and me:

4 Critters, clocks, and researrch:

5 Ideas and a fish:

6 A little physics:

7 A lot of history:

8 Still more history:

9 America, attitudes, and making sense:

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