The Appendix/Cave Fish Eyes/Etc. are (NOT) vestigial


#81

And if the intelligent designer is working so hard and doing such a masterful job of fooling us into thinking evolution is real, why not go along with it?


#82

The function of the caecum in many species is to digest cellulose, and the appendix is a part of that organ.


#83

True. In horses and many other species the cecum serves as a “fermentation vat” where microbes break down cellulose from plants, which otherwise couldn’t be digested. But some species (cows and other ruminants) are foregut fermenters. But them we have poor bunny rabbits and beavers. By the time their food is fermented in the cecum it’s too late to absorb it, so they have to eat their own poop! I’m not kidding. (Such great design!) Bunny rabbits


(Ashwin S) #84

I am guessing , by your definition that the appendix cannot be considered vestigial in any extant species.

I think it demonstrates that traits that disappear can reappear provided the circumstances demand it.This is not the darwinian model. Its more Lamarckian. Besides, i have already said that i believe organisms have some level of ability to adapt to their circumstances (This includes loss and gain of function).I just think blindly describing something as vestigial just because we don’t know its function is wrong.

What you posted is just a small part of their study and the overall conclusions dont change because of it.I don’t see how you assume the appendix was vestigial at some point. Can you name the organism for which it was vestigial?
This is just more speculation.In fact, you are claiming to know more than the authors here :slight_smile:

Actually i was skeptical about evolution long before i became a christian or even read the OT.
I am asking questions that should arise. If a study shows the appendix keeps on emerging, there are two questions that need to be asked.

  1. Why (i.e is there some mechanism that makes this happen)- Scientists are asking this question.
  2. Did we make a wrong assumption?- Scientists are not asking this question.

Pls don’t project your experience on me!

This is a result of circular reasoning. There is no way the appendix disappearing and appearing 29+ times in mammals is a prediction of evolution. Its against the very idea.

Things like the appendix being found across the family tree without any single common ancestor is very much in line with the idea of a designer.
Think LED lights. They show up wherever they are needed and disappear when they are not.

Having no explanatory framework is better that a large “explanatory framework” rife with circular reasoning and pretty much unproveable assumptions. Because this so called explanatory framework doesn’t explain anything.( because it expains everything- if the

@T_aquaticus - The appendix is a separate organ.

I suggest you read and understand my comments before making ridiculous assertions.We do not have an abundance of intermediate fossils.
If you need a 100 dollars to buy something and all you have in hand is 20 cents, would you call it an abundance??
There should be atleast 100s of intermediate fossils while we have just a handful with us.

Re processing is a common practice in design.Besides, its not exactly their poop.


#85

Wouldn’t it be better to process food you eat the first time through?

No, it isn’t exactly poop but is close enough. Would you want to eat something that was part of your own defecation? Neither would I.


#86

Although fossilization is relatively rare, we really do have an abundance of fossils. I’ve seen plenty of them.


(Matthew Pevarnik) #87

And you’d be incorrect. I don’t actually know if the appendix is fully vestigial in any extant species but we would know thousands and thousands of generations from now which extant species had a vestigial appendix.

But the cave fish’s eyes DO NOT reappear and start functioning when they’re removed from the cave. Lamarkian evolution has been falsified - organisms do not just start gaining traits and losing traits as they ‘adapt’ to their circumstances when something ‘is needed.’ Where do you get that idea from?

Sure: look at their updated tree. Pick any part, let’s go with the Strepsirhini branch. Follow a black line and when it turns to a white line, they’ve lost their appendix. Tadaa- it was an organ that was positively selected for in past generations/ancestors and then in later ones the organ was lost because it stopped being positively selected for, i.e. vestigial before disappearing. Now vestigial organs don’t even have to disappear completely, as they can be re-purposed but I personally couldn’t conclude what the appendix did in an obvious way like the cave fish’s eyes.

Again you misunderstand science and what scientists do. I’ve tried to correct this so many times I give up. You say you know what scientists do, don’t do, and need to do better than scientists themselves (myself included). You are doing what I’m saying but can’t see it. You read scientific papers and think you know and can figure out the science better than the researchers, nearly all of them that we’ve spoken of in these threads. You accuse them of being so biased and ignoring conclusions that are right in front of their eyes because YOU know better. You don’t Ashwin, I’m sorry. If you want to speak so confidently on these things, go get your PhD in one of these fields and start publishing your ideas.


#88

How so? That seems to be more of a bare assertion than anything else.


(Chris Falter) #89

Thanks for sharing that paper Ashwin. It affirms everything I have stated because…

  1. The ability to interbreed the blind lineages and sighted lineages from nearby populations shows that they have common ancestry.
  2. That sight can be restored by interbreeding different blind lineages shows that (a) the blindness alleles are recessive, and (b) the eyes in blind lineages are vestigial.

Q.E.D. !!

Thanks for sharing such strong evidence for my argument.

Have a blessed day.

Chris


(Ashwin S) #90

If the appendix had a function that reduced as a lineage progressed, you would be able to predict/identify its vestigiality in specific species. The people who wrote the paper could not find any evidence of this happening. That is why they said the appendix is not vestigial.
Why can’t you leave it at that? is there some compelling reason to based on available evidence to believe the appendix is vestigial?

It was an intuition. Found a paper that describes eyeloss in cave fish as epigenetic… i.e the fish have all the information to develop sight. There are chemical tags that do not allow the eye to develop.
Since we do not see organisms loose or gain functions at the drop of a hat, there must be some thing that triggers these changes. Environmental impact on epigenetics is established … may be there are other facts too.
I wouldn’t bet on chance though.

Blockquote
Here we show that excess DNA methylation-based
epigenetic silencing promotes eye degeneration in blind cave Astyanax mexicanus.
By performing parallel analyses in Astyanax mexicanus cave and surface morphs
and in the zebrafish Danio rerio, we have discovered that DNA methylation
mediates eye-specific gene repression and globally regulates early eye development.
The most significantly hypermethylated and down-regulated genes in the cave
morph are also linked to human eye disorders, suggesting the function of these
genes is conserved across the vertebrates.
Blockquote

We dont know whether its natural selection that drives the change. I think it will end up something similar to the cavefish. i.e connected to gene regulation as opposed to random mutation.

I am not forcing any scientist to change his views or directing anyones research. However if someone presents an idea to me, i go through it myself and come to my own conclusions irrespective of how many PHDs he or she has.
I mentioned a question scientists are asking and one they are not asking. That’s a fact and i assume you are not disputing it.Now if evolution is something that can be understood only by select people with PHDs (Excluding ID scientists and creationists with PHDs); then its one of a kind.


(Ashwin S) #91

Did you drop the “intermediate” before the term fossils by mistake? or are you agreeing to my point that there are not as many intermediate fossils as there should be?

Ya, but the rabbit doesn’t mind.
Besides, even human beings process sewage water to reuse it… its just a difference in degree. Obviously this doesn’t cause sickness in the animal, so there is no negatives other than psychological impact on human beings, who really have nothing to do with it.


(Ashwin S) #92

Glad you liked the paper.Two clarifciations -

  1. The ability to interbreed shows that both fish belong to the same species. So the question of a common ancestor is mute.
  2. Further study has revealed that the eyes lost function due to epigenetic factors…
    I don’t know if the epigenetic changes are due to environmental stimuli or accidental mutation followed by selection. It will be interesting to see how this progresses.
    https://www.biorxiv.org/content/biorxiv/early/2017/10/05/199018.full.pdf

Hope you like this paper too…

God bless.


(Ashwin S) #93

I have shared enough material that should have made that clear by now.
There are organisms with a cecum and no appendix. i have shared a peer reviewed paper which documents several mammals having a cecum and no appendix.If both were the same organ, such a study would be impossible.
The Appendix has an immune function while the cecum has a digestive one.
The assertion without evidence is to say that the appendix and cecum are the same organ.

Why the desperation to prove the appendix in human beings is vestigial? The theory evolution does not stand or fall on this…

I am really surprised there is such a long debate on this issue.


(Matthew Pevarnik) #94

Besides determining if it was there for a species who lived beyond a million years ago, determining function is quite another ballgame so the notion of mapping progression into vestigiality is challenging in that sense. But that’s not how vestigial structures therefore are typically identified. Do you know how they are typically identified?

Yes but Ashwin, even if the cave fish go to a different environment… they do not develop sight. Epigenetics doesn’t work like a magical Lamarkian way to change species around. I’m not sure how you are reading these papers but all that it says is their eye genes lose their function via methylation induced by other genes and such hyper methylation and other down-regulated genes also are linked to other eye disorders in many different vertebrates. Why would this be the case? Because vertebrates have this interesting link of common descent of course!

They do regularly ask and question assumptions. All the time! When you publish a paper, that is one of the things that by default you have to check. But after a certain point, and continually testing such assumptions you don’t need to question the same assumptions time and time again since they have been tested thousands and thousands of times. It is certainly not a fact that I would grant because it’s not a fact, it’s simply untrue. And thus, it would be a false accusation of something that scientists do not do and why I said to you that you are coming in to their research and basically telling them ‘eh, you’re doing it wrong, coming to the wrong conclusions, and full of evolutionary bias.’ That means that you know better than them.

Plenty of non-scholars understand evolution, that’s not even true so I don’t know why you would even say that. What I was trying to say though is that you are claiming to have superior understanding to scientists on all their own papers.

What I will say next is the main thing that ID scientists and creationists with PhDs fail to understand: how you actually convince the scientific community of anything is not through blog posts and books, claiming you have superior understanding to the people actually doing the research. You need to actually publish your ideas and models in scientific literature! You think that common descent is false: come in and publish papers that make predictions and specify mechanisms of how things truly work. But… they don’t do this, ever. So I am trying to give you some advice in this area.


(Chris Falter) #95

Absolutely, it’s a great contribution. Biologists have shown that methylation is inherited, such that methylated cytosine is sometimes referred to as “the fifth base.” This explains why cavefish raised in aquariums do not regain their sight even after multiple generations. Your portrayal of the patterns of change as “Lamarckian” is based on an erroneous conflation of Lamarckianism and genetics.

As far as I can tell as a non-biologist, methylation is less stable than other types of mutation. This is why it is able to contribute to phenotypic changes more quickly than other types of mutations. With some very small probability demethylation can also occur. However, the breeding of cavefish in well-lit aquariums shows this to be unimportant in the short term.

The portrayal of evolution that emerges from cross-species studies is that some phenotypic changes result in the (relatively) short term from epigenetics. These can be subsequently be fixed through genetic mutations. Allow me to quote a passage from Gore and Weinstein’s paper that you might have missed:

Our findings indicate that eye loss in Pachón cavefish occurs via distinct molecular mechanisms compared to naked mole rats, where inactivating mutations are found in multiple key eye genes. This could reflect differences in their evolutionary timescales. Cavefish evolved over the past one to five million years, while naked mole rats evolved seventy-three million years ago, allowing sufficient time to fix and select acquired mutations in genes essential for eye development.

Finally, it is quite beyond me how this paper could even begin to refute that the cave lineages of A. mexicanus have vestigial eyes. The eyes of the cavefish are vestigial, and this trait is passed by inheritance from one generation to the next. The paper you cite affirms this. Q.E.D., again.

I would welcome any clarifications from members of the scientific community if this post contains any misunderstandings.


#96

That doesn’t change the fact that an appendix is a part of some caecums.

Why the desperation to prove that the appendix is not vestigial?


(Steve Schaffner) #97

I think you’ve misunderstood the finding here. The paper is proposing an epigenetic mechanism through which eye development is altered in these cave fish, but the mechanism itself almost certainly has a genetic basis. That is, there was a genetic mutation that increased expression of a protein that causes methylation of certain DNA sites, with the result that genes involved in eye development are down-regulated and the eyes don’t really develop. It’s the genetic change that is inherited, not the methylation of the eye genes. The developmental pattern should therefore be stable however the fish are raised, since the underlying change was to DNA.

There’s a lot of confusion sloshing about these days about epigenetics. Saying some process occurs through an epigenetic mechanism tells us very little, in fact, since nearly everything in development occurs through an epigenetic mechanism. The danger is in hearing “epigenetic mechanism” and thinking “trans-generational epigenetic mechanism”. Trans-generational inheritance of epigenetic marks seems to be unusual in animals and is of uncertain evolutionary significance.


#98

Don’t be silly. We have lots of intermediate fossils, even though fossilization is a rare event. How many do you think there should be? -show your calculations.

Do you examine the fossil evidence yourself or just look at pictures and ID creationist web sites? Did you get to the traveling exhibition “Whales: Giants of the Deep” which originated at the Museum of New Zealand Te Papa Tongarewa? It was at the AMNH in NYC. It was wonderful opportunity to see ancient and modern whales.

The point is, obviously, that it is terrible design! Unless God is a jokester.


(Chris Falter) #99

Thanks so much for clarifying the concepts, Steve!


(Ashwin S) #100

Why dont you tell me… i wouldnt be surprised if there is some ammount circular reasoning involved.

Scientists who actually work on cave fish disagree with you. They claim, that blind cave fish can develop sight. Let me quote a guy who has published quite a no: of peer reviewed papers on this species…

Blockquote
An example of the morphological differentiation among individuals of the same species is the case of the characid fish Astyanax fasciatus, a tetra that inhabits the Sótano del Caballo
Moro cave in Mexico. At some unknown time in the past, part of the ceiling of that cave collapsed, allowing light to illuminate part of one of its underground lakes. Blind, depigmented
individuals are found preferentially in the dark side, while eyed, pigmented fish are found in the illuminated side. Interestingly, genetic analysis revealed that the cave-dwelling eyed fish is closer to the blind fish than to the surface population. This finding suggests that the cave eyed fish were originally members of the cave population and reacquired eyes and pigmentation following the collapse of the cave ceiling and exposure to the light.
Blockquote
He further describes the below experiment:
Blockquote
My collaborators and I were able to confirm these initial observations by controlling the light conditions for 24-hour-old larvae of A. fasciatus from three different populations: epigean
(eyed, pigmented), troglomorphic (blind, depigmented) and their hybrids. For a period of 30 days, some of the larvae were exposed to light 24 hours per day, others were confined to total darkness.The results showed that the eyes of the epigean larvae were much less
developed when the fish were raised under conditions of total darkness than when raised under constant light. However, the most spectacular results were obtained with the cave population: Although those larvae that were raised under conditions of total darkness
did not show any noticeable eye tissue, as expected, those raised under constant light conditions did. This result strongly suggests that many troglomorphic animals evolved
from epigean species by means of phenotypic plasticity.
Blockquote

Blockquote
This biological picture is complicated not only in space but also in time. When the troglomorphic form of A. fasciatus was originally described in 1936, the entire population in that locality consisted of a very uniform morph of blind and depigmented fishes. I analyzed
the gross morphology of individuals that had been collected between 1936 and 1942 as well as those I collected in 1982. I found that the La Cueva Chica population had evolved in 43 years or less into a morphologically intermediate population composed of individuals
that were neither totally blind and depigmented nor fully eyed and pigmented. I concluded that this new morph was the result of introgressive hybridization—transfer of genes from
one population to another via repeated crosses. The transfer probably started in
1940 with the invasion of the cave environment by epigean individuals.
Blockquote
Source:http://www.aromerojr.net/Publications/570.American%20Scientist.pdf

i think its very likely that blind cave fish populations which are exposed to light develop fully functional eyes within a few generations.
@glipsnort : you might find the above information interesting
@Chris_Falter:
Pls go through the above material.Would you call a trait that does not extend across a species and might appear and disappear according to environmental conditions/cross breeding a vestigial trait?
I wouldn’t.

I think books do have an impact on scientists though the major target are the general public. As to peer reviewed papers, ID scientists do show an interest to participate in this dialogue through peer reviewed papers. They claim to face difficulties because of censorship and show examples of the same.They have even started a Journal to publish peer reviewed papers. How much other scientists will interact with them is indeed a question mark. You can get their perspective from the below article.
https://evolutionnews.org/2010/05/biocomplexity_a_new_peerreview/

As for me, I have a career in Engineering (Design) which i enjoy a lot and have no plans to switch streams and get into biology. Though i do reserve the right to evaluate any claims i come across and form my own independent opinion. And i will not hesitate to speak what i believe and am willing to justify why i believe so.

I have given you clear documented reasons why the Appendix is not a part of the caecum. Pls corroborate your claims with information (i.e- What makes teh appendix part of the cecum, evidence for shared function etc).

Since you claim an abundance… why dont you show me your calculations… or is it that evolutionary scientists dont need a mathematical basis for any of their claims?

Obviously to whom? Have you ever designed anything in your life? The rabbits digestive system is for the rabbit… not for human beings. So measuring its design quality based on Human biases is not smart.