How does evolution overcome genetic hurdles?

Open Forum Scientific Evidence
#1

Hi,

During my diploma studies in Life Sciences, I learnt about 3 things that act against mutation, which is the mechanism for genetic changes:

  1. Presence of DNA repair mechanisms
  2. Genetic diseases - more than often mutations lead to non-functional proteins or diseases.
  3. Absence of means to insert base pairs on a large scale

Doesn’t (2)+(3) = prevent the accumulation of genetic changes over time? Won’t (1) reduce the rate of mutation greatly?

Also, I do see that many biochemical pathways are irreducibly complex. For example, the transcription of a protein from DNA.

I do understand that dogs descended from wolves but the fossil record shows us that 300,000 years ago, wolves existed and are largely unchanged from modern-day wolves.

My question is how do the evolutionists account for the above hurdles? Won’t the points I mentioned 1-3, work greatly against evolution which requires a great amount of information to be inserted for e.g a gill-breathing fish to acquire lungs?

Honest questions

Thanks
David

#2

(2) prevents (usually) the accumulation of deleterious genetic changes over time, but does nothing to prevent the accumulation of neutral and beneficial changes. (1) does indeed reduce the rate of mutation greatly, and has been doing so for hundreds of millions of years. That is, it reduces it to the mutation rate we observe, which is plenty high enough to generate lots of genetic variation and lots of evolution.

(3) is wrong. There are processes that insert base pairs on a large scale: large duplications, including whole-genome duplications. But the vast majority of evolution does not require such large insertions of DNA.

Nothing prevents the evolution of irreducibly complex biochemical pathways. Transcription is so ancient that it’s impossible to determine exactly how it arose, but it is worth noting that the core of the transcription process, the central component of the ribosome, is not itself a protein.

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#3

My problem with the part about random changes accumulating in the genome is that a genome is basically a coded program. This webpage is coded by javascript. If I opened up the javascript for this page and randomly added in scripts at random places…it won’t evolve this forum into ESPN.soccernet.com.

More than likely, the webpage will stop functioning.

What I meant about irreducible complexity is that if you took each metabolic pathway apart, they would serve no function. I think Wikipedia might have better examples:

https://en.wikipedia.org/wiki/Irreducible_complexity#:~:text=Irreducible%20complexity%20(IC)%20is%20the,less%20complex%20system%20would%20function.

Sorry I left school a long time ago, I can’t remember all the details.

#4

Which is a good reason why evolution never works that way. It’s always small and incremental accumulations in populations over much time. Never a tornado-junkyard-assembled 747 or a random addition of a code bit turning one bit of code into some entirely different functioning one.

I think I’ve also heard biologists here criticize the whole comparison between DNA and computer code, so it may be a very limited analogy in terms of how far it can be pressed.

#5

Lycopods have not changed a lot either over a much longer time. But some of the plants changed big time. So while wolves may or may not have changed that much, we can see how ancestral Caniforms have evolved including into wolves, bears, and so on. Clams have not changed a whole lot either.

Most ferns seem to have the same basal traits as their ancestor but we also see some that had changed a lot. Some of the filmy aquatic ferns, the underground ferns, and so on.

So arguing wolves have not changed very much means very little.

#6

No it is not! It is nothing like a coded program. It is an accumulation of random changes where the outright harmful ones have been weeded out. Most serve no purpose whatsoever. Others make changes with no impact on survival. And only a few serve a positive role in the survival of the species.

Some people like to overextend the evolutionary paradigm to describe things like programing but since the changes in programing are not random at all, its similarity is superficial. The biggest difference is that the program is much much more compact and efficient and as you are aware very sensitive to the slightest change. The genome is not compact, efficient or very sensitive to most changes since only a very small portion of the genome is actually used.

To be like a genome it would have to many times larger telling the computer running the script to ignore almost all of it. In that case most random changes would have no effect at all.

Imagine a computer script produced in similar manner. Keep trying random sections of code, throwing out the ones which crash and keeping those which do something interesting. We don’t program this way because is not a very good way to make the computer do what you want. But that doesn’t mean it doesn’t manage to do some interesting things. That is what living organisms are like.

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#7

Alright, so basically what I’m hearing is;

  1. small incremental changes occur over a long period of time
  2. there exist processes that insert base pairs on a large scale
  3. harmful changes are weeded out
  4. genome is not sensitive to changes ( this is not what I was taught, a single change in a base pair can render an entire enzyme disfunctional)

and this overcomes the 3 hurdles I highlighted.

I was taught things like “apoptosis”, also known as “programmed cell death”. The genome is a program that controls all the functions of the cells by providing instructions to the cell via mRNA -> proteins/enzymes.

#8

This might help a little:

#9

As others have noted, DNA really isn’t much like a computer program – and this is speaking as a computational biologist. Computer programs are, as you say, quite brittle and almost always fail when subject to random changes. They’re also generally brittle in other ways: feed them data formatted incorrectly and most will choke, for example. Organisms, on the other hand, are quite robust to all kinds of inputs and to lots of random changes, as long as the changes aren’t too big. (Not all change, of course – plenty of mutations are quite deleterious, but those are weeded out by natural selection.) The two kinds of robustness are connected: cells have to be able to function with more or less of various resources, for example, which makes them robust to mutations that change how genes are regulated and thereby change the amount of various proteins present.

This robustness is evident when you consider the substantial variation that is present in any species. Lots of slightly different versions of genes and gene regulatory elements produce organisms that vary in size, shape, strength, color, metabolic capacity, etc – and yet all function just fine. That variation is all produced by random mutations, which clearly have not broken the program, so to speak. The same variation provides the raw material for most evolution, since it means that a species can change in response to new selective pressures, with some variants being favored and coming to dominate the population,

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#10

Thanks for the replies Steve,

since it means that a species can change in response to new selective pressures, with some variants being favored and coming to dominate the population,

I have no problem with this. It’s all observable - dogs descended from wolves. Dogs are a genetic variant of wolves. The ancestor of the whale was a land-dwelling mammal. Whales are a genetic variant of a particular mammal. (Doesn’t this gel closely with what we read in Genesis that all creatures were created according to their “kinds”?).

But for a fish with gills to evolve into a land-dwelling animal that breathes through lungs - it would need a new set of “programs/instructions” for the lungs and the metabolic pathways associated with it. I really can’t see how this can happen by random chance given an infinite amount of time. Is there any compelling evidence that this can happen (e.g AI simulations)? Is Tiktaalik the only transitional fossil available to us?

No offence intended. I not trying to question your knowledge. I’m just a weekend science-hobbyist who is trying to understand and learn.

#11

Steve may critique this and blow it out of the water (@glipsnort, or anyone else) :slightly_smiling_face:, but I would actually like some feedback on this crude analogy of neutral drift, and maybe suggest some additions or other alteration… or complete deletion :slightly_smiling_face::

Imagine a long string of scrambled letters with no intelligible words that can be parsed out to impute meaning to any partial sequence. But suppose ‘each generation’, several mutations occur. It wouldn’t necessarily take many generations for an intelligible sequence to ‘fall out’, so to speak, and the ‘reader bot’ to transcribe it into something with utility.

That is kind of how I envision neutral drift to work to produce novel function or morphology. (Does that play at all, Steve?) That is speaking very much as a layman whose last biology course was Bio 101 taken postbaccalaureate to fulfill the pre-med curriculum thirty years ago (I already had one semester of zoology), no biochem (not even one semester was required back then), and certainly no evolution.

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#12

Sure, but that pattern doesn’t stop there. Wolves and whales are both genetic variants of mammals, and all mammals are genetic variants of amniotes, and all amniotes are genetic variants of tetrapods, and all tetrapods are genetic variants of vertebrates. The same pattern, supported by the same kinds of evidence.

We can’t simulate the actual evolutionary process in that kind of transition because we don’t know nearly enough about the genetic basis for most of the relevant traits. What we do know is that the transition could have occurred through many small steps, many of which we have evidence for (see https://en.wikipedia.org/wiki/List_of_transitional_fossils#Fish_to_tetrapods for a list of transitional fossils). We have fish alive today that take in some oxygen by breathing into simple air sacs, and fish that breathe through more complex organs with lots of sacs, i.e. lungs (hence the name ‘lungfish’). So that ability was likely present long before any intermediates started venturing out of the water. Based on fossil evidence, skeletal changes also started earlier, probably to permit shallow-dwelling, air-breathing fish to push along the bottom with their fins, which then led to fish that had rudimentary legs that couldn’t bear their full weight. And we still have amphibians today that have both lungs and gills. So where do you think the unsurmountable obstacle is?

No offense taken. Note that I know a fair bit about genetics but have no expertise in fossils or in the evolution of tetrapods.

ETA: And I see that the first analysis of a lungfish genome has just been published: https://www.nature.com/articles/s41586-021-03198-8

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#13

Neutral drift does indeed churn out all kinds of stuff. What’s critical is that novelties that have some kind of minimal utility can be stabilized and then improved by natural selection. Otherwise the rudimentary features would just churn away again.

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#14

At the Darwin exhibition at the American Museum of Natural History they had real mudskippers. Fascinating little fellows!

#15

400 years ago, people couldn’t see how ice particles moving around in clouds could produce lightning. Reality has this strange property of not caring what we can or can’t imagine.

Ichthyostega and Acanthostega come to mind. There are also living lungfish that have both gills and a lung.

#16

Jenga might be a useful analogy, if you have ever played the game. When you start the game there are blocks that can be easily removed, and removing them would be neutral to keeping the tower upright. However, as the game moves along those blocks that could have been removed at the beginning are now vital to the tower staying upright and can no longer be removed. You also have new blocks being added to the top which changes the interactions throughout the tower. Also consider how each game is different because slightly different starting conditions and different block choices along the way change which blocks are important. This is similar to how genes interact with one another, how amino acids interact with one another within the same protein, and how bases interact with each other in both DNA and RNA. It is also similar to the contingent nature of evolution where certain changes in the past can influence which changes in the future are important.

I think it is also important to remember that interactions in biology are physical and chemical which is a bit different than words on a page. The page of a book doesn’t bend in the middle so complementary letters on the outside of the page can form hydrogen bonds between them, as one example.

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#17

Thanks for the enlightenment

#18

Thanks for that! The stability aspect with successive changes makes it a good metaphor.

#19

That can happen, but is not usually the case. For a current example, think of the spikes on the COVID virus. Some variations to that protein are indifferent, and others enhance cellular binding. This is very typical of much microbiological functioning - more modulating than binary.

#20

The swim bladder of standard bony fish is basically a modified lung. As noted above, the lung was present in fish before they started to use a crawling type of locomotion. Also, any moist surface can be used for breathing if it is permeable to oxygen. Many amphibians manage without lungs or gills, and many fish breathe oxygen through their skin or through the mouth and gut, if they gulp air. Hibernating pond turtles get enough oxygen from water through the cloacal lining. So a gill to lung transition is not that hard; millions of tadpoles manage it every year. Air has much more oxygen than water, especially if the water is stagnant, so there’s an advantage to having even rather rudimentary capability to get some oxygen from air.

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