Nervous system in the cards

Years and years go by and front-loading evolution remains plausible.

This is an important paper, for it uses a novel method to show that the outgroup to all other animals is not sponges, as most people thought, but ctenophores. And that implies that nerves and muscles evolved twice independently. https://t.co/fLoJ7tN0GE

— Jerry Coyne (@Evolutionistrue) May 20, 2023

From the paper:

However, in the ctenophore-sister scenario supported here by deeply conserved syntenies, there are two possible alternatives explaining the evolution of neurons: either complex neural systems arose more than once^3,59,62 but were elaborated differently in ctenophores, cnidarians and bilaterians^3,4,59, or neuronal cell types were present in the metazoan ancestor but were lost in the sponge lineage^4,9,63.

The emergence of the nervous system doesn’t look like some freak accident.

10 signs of Intellectual Honesty.

When it comes to just about any topic, it seems as if the public discourse on the internet is dominated by rhetoric and propaganda. People are either selling products or ideology. In fact, just because someone may come across as calm and knowledgeable does not mean you should let your guard down and trust what they say. What you need to look for is a track record of intellectual honesty. Let me therefore propose 10 signs of intellectual honesty.

1. Do not overstate the power of your argument. One’s sense of conviction should be in proportion to the level of clear evidence assessable by most. If someone portrays their opponents as being either stupid or dishonest for disagreeing, intellectual dishonesty is probably in play. Intellectual honesty is most often associated with humility, not arrogance.

2. Show a willingness to publicly acknowledge that reasonable alternative viewpoints exist. The alternative views do not have to be treated as equally valid or powerful, but rarely is it the case that one and only one viewpoint has a complete monopoly on reason and evidence.

3. Be willing to publicly acknowledge and question one’s own assumptions and biases. All of us rely on assumptions when applying our world view to make sense of the data about the world. And all of us bring various biases to the table.

4. Be willing to publicly acknowledge where your argument is weak. Almost all arguments have weak spots, but those who are trying to sell an ideology will have great difficulty with this point and would rather obscure or downplay any weak points.

5. Be willing to publicly acknowledge when you are wrong. Those selling an ideology likewise have great difficulty admitting to being wrong, as this undercuts the rhetoric and image that is being sold. You get small points for admitting to being wrong on trivial matters and big points for admitting to being wrong on substantive points. You lose big points for failing to admit being wrong on something trivial.

6. Demonstrate consistency. A clear sign of intellectual dishonesty is when someone extensively relies on double standards. Typically, an excessively high standard is applied to the perceived opponent(s), while a very low standard is applied to the ideologues’ allies.

7. Address the argument instead of attacking the person making the argument. Ad hominem arguments are a clear sign of intellectual dishonesty. However, often times, the dishonesty is more subtle. For example, someone might make a token effort at debunking an argument and then turn significant attention to the person making the argument, relying on stereotypes, guilt-by-association, and innocent-sounding gotcha questions.

8. When addressing an argument, do not misrepresent it. A common tactic of the intellectually dishonest is to portray their opponent’s argument in straw man terms. In politics, this is called spin. Typically, such tactics eschew quoting the person in context, but instead rely heavily on out-of-context quotes, paraphrasing and impression. When addressing an argument, one should shows signs of having made a serious effort to first understand the argument and then accurately represent it in its strongest form.

9. Show a commitment to critical thinking. ‘Nuff said.

10. Be willing to publicly acknowledge when a point or criticism is good. If someone is unable or unwilling to admit when their opponent raises a good point or makes a good criticism, it demonstrates an unwillingness to participate in the give-and-take that characterizes an honest exchange.

While no one is perfect, and even those who strive for intellectual honesty can have a bad day, simply be on the look out for how many and how often these criteria apply to someone. In the arena of public discourse, it is not intelligence or knowledge that matters most – it is whether you can trust the intelligence or knowledge of another. After all, intelligence and knowledge can sometimes be the best tools of an intellectually dishonest approach.

 

Nick Lane Lecture

Enjoy this lecture, as it echoes many of the points i have made on this blog:

Humans and Birds Use Same Mechanism to Produce Sound.

Birds and humans look different, sound different and evolved completely different organs for voice production. But now new research published in Nature Communications reveals that humans and birds use the exact same physical mechanism to make their vocal cords move and thus produce sound……

Švec: “To me it was very surprising and fascinating to discover that such different vocal organs make sound in the same way”.

According to Elemans the new discovery not only sheds new light on the sophisticated vocal talents of song birds. The discovery is also interesting and useful because it can be paired with the knowledge about another interesting vocal mechanism shared by some birds and humans: The neural mechanisms underlying vocal learning. Both songbirds and humans are not born with the ability to speak or sing, but must learn their language or song by listening to others, a process called vocal imitation learning or simply vocal learning.

HERE

How to Design Evolution

My hypothesis of front-loading evolution begins with a simple question – would it be possible to design/guide evolution given the reality of random mutations and selection? Then, if so, HOW might one do this?

Richard Thaler and Cass Sunstein wrote a book entitled Nudge that advocated for a soft version of social engineering.  I have not read the book, but there is a short interview on Amazon.com that cites what I think to be most relevant:

 

Amazon.com: What do you mean by “nudge” and why do people sometimes need to be nudged?

Thaler and Sunstein: By a nudge we mean anything that influences our choices. A school cafeteria might try to nudge kids toward good diets by putting the healthiest foods at front. We think that it’s time for institutions, including government, to become much more user-friendly by enlisting the science of choice to make life easier for people and by gentling nudging them in directions that will make their lives better.

 

And

 

Amazon.com: What is “choice architecture” and how does it affect the average person’s daily life?

Thaler and Sunstein: Choice architecture is the context in which you make your choice. Suppose you go into a cafeteria. What do you see first, the salad bar or the burger and fries stand? Where’s the chocolate cake? Where’s the fruit? These features influence what you will choose to eat, so the person who decides how to display the food is the choice architect of the cafeteria. All of our choices are similarly influenced by choice architects. The architecture includes rules deciding what happens if you do nothing; what’s said and what isn’t said; what you see and what you don’t. Doctors, employers, credit card companies, banks, and even parents are choice architects.

We show that by carefully designing the choice architecture, we can make dramatic improvements in the decisions people make, without forcing anyone to do anything. For example, we can help people save more and invest better in their retirement plans, make better choices when picking a mortgage, save on their utility bills, and improve the environment simultaneously. Good choice architecture can even improve the process of getting a divorce–or (a happier thought) getting married in the first place!

 

 

A NYT article explains a very interesting example of nudging:

 

THE flies in the men’s-room urinals of the Amsterdam airport have been enshrined in the academic literature on economics and psychology. The flies — images of flies, actually — were etched in the porcelain near the urinal drains in an experiment in human behavior.

After the flies were added, “spillage” on the men’s-room floor fell by 80 percent. “Men evidently like to aim at targets,” said Richard Thaler of the University of Chicago, an irreverent pioneer in the increasingly influential field of behavioral economics.

Mr. Thaler says the flies are his favorite example of a “nudge” — a harmless bit of engineering that manages to “attract people’s attention and alter their behavior in a positive way, without actually requiring anyone to do anything at all.” What’s more, he said, “The flies are fun.”

 

So why mention any of this on The Design Matrix?

Amoeba now support front-loading evolution

 

I told you tyrosine kinases were old. It has now been discovered in amoeba, along with machinery to help front load the emergence of the immune system:

From Clarke M et al., Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling.  Genome Biol. 2013 Feb 1;14(2):R11

BACKGROUND: The Amoebozoa constitute one of the primary divisions of eukaryotes encompassing taxa of both biomedical and evolutionary importance, yet its genomic diversity remains largely unsampled. Here we present an analysis of a whole genome assembly of Acanthamoeba castellanii (Ac) the first representative from a solitary free-living amoebozoan.

RESULTS:

Ac encodes 15,455 compact intron rich genes a significant number of which are predicted to have arisen through interkingdom lateral gene transfer (LGT). A majority of the LGT candidates have undergone a substantial degree of intronization and Ac appears to have incorporated them into established transcriptional programs. Ac manifests a complex signaling and cell communication repertoire including a complete tyrosine kinase signaling toolkit and a comparable diversity of predicted extracellular receptors to that found in the facultatively multicellular dictyostelids. An important environmental host of a diverse range of bacteria and viruses, Ac utilizes a diverse repertoire of predicted pattern recognition receptors many with predicted orthologous functions in the innate immune systems of higher organisms.

CONCLUSIONS:

Our analysis highlights the important role of LGT in the biology of Ac and in the diversification of microbial eukaryotes. The early evolution of a key signaling facility implicated in the evolution of metazoan multicellularity strongly argues for its emergence early in the Unikont lineage. Overall the availability of an Ac genome should aid in deciphering the biology of the Amoebozoa and facilitate functional genomic studies in this important model organism and environmental host.

Remind me again why I am supposed to be wrong about the hypothesis of front-loading evolution?

Is evolution predictable? To a surprising extent the answer is yes.

In chapter 7 of The Design Matrix, I have a section entitled, “Unpredictably Predictable.”  The basic argument is summarized in the last sentence of that chapter:

Even though evolution is supposed to be inherently unpredictable, as we can see, it has occurred within a very predictable biological matrix.

Evolution is not some random “free-for-all” where anything that just happens to work will eventually be selected for.  Evolution is a biological process that is constrained and thus channeled by the composition and arrangement of life’s machinery.

I then spell out one aspect of this evolution in a section entitled, “Designed to Redesign.”  Here I talk about the essential role that gene duplication plays in the function we call “evolution”:

It is a beautiful solution for a front-loading designer. In one process, we both propagate the original design and set things up to unpack secondary designs without erasing the original design. Stability and change, all in one package. As an added bonus, the infl uence of contingency is dampened. It does not matter if some or many gene duplication events drift off in unintended fashion (most will merely tweak the original function or decay away). Th e beauty of gene duplication is that it explores sequence space while retaining and propagating the original sequence. As long as the original sequence is essentially retained somewhere, someplace, evolution gets to “try again” over and over and over in its rigged search for some future design. In other words, if a designer wanted a secondary design to unpack itself in an animal cell, duplication of the original sequence is bound to happen in all cells, including animal cells. When it eventually occurs in an animal cell, the stage is set to unpack the secondary design. If it fails, we need only wait until the next round of duplication and mutation occurs. It is the intelligent use of chance.

Over five years later, a paper has appeared in the journal Science that adds even more plausibility to my perspective.  Enjoy:

Neuron, Muscle, and Front-loading

Well, it’s been almost four months since I last updated this blog. The nice thing about the hypothesis of front-loading is that with the passing of time, and the acquisition of new data, the hypothesis becomes increasingly plausible. Consider this:

A previous sequencing of the genome of the Amphimedon queenslandica — a sponge that lives in Australia’s Great Barrier Reef — showed that it contained the same genes that lead to the formation of synapses, the highly specialized characteristic component of the nervous system that sends chemical and electrical signals between cells. Synapses are like microprocessors, said Kosik explaining that they carry out many sophisticated functions: They send and receive signals, and they also change behaviors with interaction — a property called “plasticity.”

“Specifically, we were hoping to understand why the marine sponge, despite having almost all the genes necessary to build a neuronal synapse, does not have any neurons at all,” said the paper’s first author, UCSB postdoctoral researcher Cecilia Conaco, from the UCSB Department of Molecular, Cellular, and Developmental Biology (MCDB) and Neuroscience Research Institute (NRI).

This time the scientists, including Danielle Bassett, from the Department of Physics and the Sage Center for the Study of the Mind, and Hongjun Zhou and Mary Luz Arcila, from NRI and MCDB, examined the sponge’s RNA (ribonucleic acid), a macromolecule that controls gene expression. They followed the activity of the genes that encode for the proteins in a synapse throughout the different stages of the sponge’s development.

“We found a lot of them turning on and off, as if they were doing something,” said Kosik. However, compared to the same genes in other animals, which are expressed in unison, suggesting a coordinated effort to make a synapse, the ones in sponges were not coordinated.
“It was as if the synapse gene network was not wired together yet,” said Kosik. The critical step in the evolution of the nervous system as we know it, he said, was not the invention of a gene that created the synapse, but the regulation of preexisting genes that were somehow coordinated to express simultaneously, a mechanism that took hold in the rest of the animal kingdom.

See? Evolution didn’t need to invent a new gene. Organisms without nervous systems had enough of the parts to make the synapse (the key component of the nervous system) and it was just a matter of time before something would trigger them to be expressed at the same time.

HT: Blas

If nervous tissue was front-loaded to exist, it would make sense to also front-load the appearance of muscle:

Introns continue to fit nicely in front-loaded evolution

In the past, I have raised the hypothesis that introns have a function – to facilitate the evolution of metazoan organisms. I raised the hypothesis here and defended it from criticism here.

A recent paper adds more support to this hypothesis:

Origin and evolution of spliceosomal introns.
Rogozin IB, Carmel L, Csuros M, Koonin EV.
Biol Direct. 2012 Apr 16;7(1):11.

Let’s go through the abstract.

Coyne vs. Shapiro

Jim Shapiro has been outlining his views on evolution over at the Huffington Post, including a posting entitled, What Is the Key to a Realistic Theory of Evolution?

Not surprisingly, Jerry Coyne does not like it and weighs in with a posting entitled, A colleague wrongfully disses modern evolutionary theory.

Let me focus on a key point of their disagreement.