What about Abiogenesis

[Jimlarmore]

When we look at living cells today we find it hard to imagine how the first cell could have happened in a fortuitous accidental way. I want to make just a few posts on major hurdles that those who would say that this is how life emerged must over come.

Let's examine some things that make unassisted abiogenesis essentially impossible. For starters life demands the complex use of thousands of biochemicals. Proteins and enzymes, which are long chains of amino acids connected by a peptide bond are extremely specific in what they do chemically. How could a protein develope over time chemically until it accidentally got it right for a living sytem and remain intack until the rest of the sytem developed so it could function?

Next Stereo-chemistry:

The chirality of amino acids are all one way ( i.e. Levo or left handed ) in living systems. In nature when amino acids are produced we always see a misture of dextro and levo or right and left handed chirality. Today all living sytems should show both right and left handed ones if life arose from accidental fortuituous combinations. This is not the case. As a matter of fact anytime a wrong handed amino acid is introduced into a living reaction it shuts it basically down.

Most proteins are made in the cell by the action of the DNA onto the RNA's in the nucleus which by the way is also chiral but right handed or dextro. Again when we rarely see nucleotides formed in nature they are always a mixture of both dextro and levo or right and left handed.

Another really big problem is that of a suitable containment system. Cells today have either a wall in plants or a membrane in animals. The first cell had to manage someway to be encapsulated with a system that could not only protect the organelles inside but be able to communicate with the outside world to draw in nutrients and expell waste etc. The cell wall and membrane are very complex structures that don't just hang around in nature to be fortuitously grabbed by a floating conglomerate of biochemicals that just accidentally got together in the right sequence.

Honestly folks, it takes more faith to believe in abiogenesis than it does to believe in fiat creation.

God Bless
Jim Larmore

 

[atomweaver]

When we look at living cells today we find it hard to imagine how the first cell could have happened in a fortuitous accidental way. I want to make just a few posts on major hurdles that those who would say that this is how life emerged must over come.

Nothing is accidental in chemistry.

Let's examine some things that make unassisted abiogenesis essentially impossible. For starters life demands the complex use of thousands of biochemicals.

Without knowing what the first living cell was , how can you assign any quantity to the number of biochemicals necessary for life? Upon what basis do you assert thousands, rather than dozens?

Proteins and enzymes, which are long chains of amino acids connected by a peptide bond are extremely specific in what they do chemically. How could a protein develope over time chemically until it accidentally got it right for a living sytem and remain intack until the rest of the sytem developed so it could function?

Proteins and enzymes were probably a late addition to life.

Next Stereo-chemistry:

Excellent! I love stereo-chemistry!!!

The chirality of amino acids are all one way ( i.e. Levo or left handed ) in living systems. In nature when amino acids are produced we always see a misture of dextro and levo or right and left handed chirality.

Not true. Introduce your reagents onto a crystalline substrate, such as calcite, or a minteral rich in titanium dioxide such as rutile or anatase, and you get an l-enatiomeric excess, which can be further enriched by natural processes. Its also interesting that depositing formamide onto titanium dioxide and exposing it to UV light can give you all of the RNA and DNA nucleotides SOURCE.

Today all living sytems should show both right and left handed ones if life arose from accidental fortuituous combinations. This is not the case.

True, this is not the case. Life did not arise from a typical homogenous mixture of nucleic acids in a glass erlenmeyer flask. It more likely happened on a mineral substrate, and started off with a small level of enantiomeric enrichment, then was further enriched by day-night cycles of reaction and chemical decomposition. Again, the products of a chemical reaction are predictable, not accidental.

As a matter of fact anytime a wrong handed amino acid is introduced into a living reaction it shuts it basically down.

What does this mean?

Most proteins are made in the cell by the action of the DNA onto the RNA's in the nucleus which by the way is also chiral but right handed or dextro. Again when we rarely see nucleotides formed in nature they are always a mixture of both dextro and levo or right and left handed.

Again, incorrect. There are simple systems which show that enantiomeric enrichment is quite easily obtained.

Another really big problem is that of a suitable containment system. Cells today have either a wall in plants or a membrane in animals. The first cell had to manage someway to be encapsulated with a system that could not only protect the organelles inside

What if the first life form simply was an organelle? Your timeline gets too far ahead of itself too quickly... the first organism you envision is vastly more complex than any that an abiogenesis researcher would suggest as a protobiont (first self-replicator)...

but be able to communicate with the outside world to draw in nutrients and expell waste etc. The cell wall and membrane are very complex structures that don't just hang around in nature to be fortuitously grabbed by a floating conglomerate of biochemicals that just accidentally got together in the right sequence.

You assume that the first living thing must be as complex as, say, an amoeba. The first life structure might have been as simple as a virus, or mitochondria, so your 'criticism from complexity' don't really withstand scrutiny, as it doesn't accurately represent any position within what little investigation is being done in the field of abiogenesis.
Your argument falls along the lines of a very intelligent re-telling of the fallacious "tornado making an airplane" argument; "what I see is too complex to have formed by accident". To continue that analogy, abiogenesis isn't looking to make an airplane... maybe a hang glider or a paper airplane, at best

Honestly folks, it takes more faith to believe in abiogenesis than it does to believe in fiat creation.

Also not true. Abiogenesis has, as of yet, nothing firm for anyone to believe in or investigate, one way or another. Its a very early scientific "work in progress". I'd challenge you to find anyone who 'believes in' it at this early stage. "Believes in what?" shoudl be the normal response. Its like critiquing a film before the first cast member has been chosen, by pretending you know just what the final movie will be like from reading the first draft script alone... I hope once it is a fully developed hypothesis, there will be something more than the usual arguments from incredulity postulated against it.

Have a great day!!

 

[juvenissun]

Without knowing what the first living cell was , how can you assign any quantity to the number of biochemicals necessary for life? Upon what basis do you assert thousands, rather than dozens?

Is it possible to have a cell made of only dozens biochemicals? I guess it is not possible today.

If so, does a single cell also evolve? From dozens elements to thousands elements?

Further, do we see the evolution of a single cell today? I am not sure what does this question mean. But it is a question, isn't it?

 

[gluadys]

If so, does a single cell also evolve? From dozens elements to thousands elements?

A single cell reproduces--if it lives long enough to do so. A population of self-replicating unicellular entities evolves.

Further, do we see the evolution of a single cell today?

We see the evolution of species of unicellular creatures, yes. A single cell, like a single organism, does not evolve. But a population does.

 

[juvenissun]

A single cell reproduces--if it lives long enough to do so. A population of self-replicating unicellular entities evolves.



We see the evolution of species of unicellular creatures, yes. A single cell, like a single organism, does not evolve. But a population does.

OK. Let me rephrase it:

Do we see one "type" (?) of cell evolved into another "type" today?

The type means something characterized the cell and if it changes, then the cell becomes different (I don't know how to characterize a significant difference in terms of evolution).

 

[gluadys]

OK. Let me rephrase it:

Do we see one "type" (?) of cell evolved into another "type" today?

The type means something characterized the cell and if it changes, then the cell becomes different (I don't know how to characterize a significant difference in terms of evolution).

Without some clear definitions, it is hard to answer the question. Is a significant difference one that arises in a single generation or the product of the accumulation of many changes that were not originally significant?

Is a significant difference one that represents a cladistic division?

Is a significant difference one that changes the behaviour of the population?

And is a significant difference what one should even be looking for?

You might do better to begin with basic population genetics and work your way from there.

But basically, any sort of evolution that occurs in complex species also occurs in unicellular species. In addition, unicellular species are more open to horizontal transfer of genetic information. So evolution in unicellular species is less dependent on inherited DNA.

 

[juvenissun]

You might do better to begin with basic population genetics and work your way from there.

You know that I will not do that. And I do not have to. Students go from lesson 1 on anything because they do not have a knowledge base. But I can jump from lesson 0.1 to lesson 20 in a few minutes, even I do not know what's said in between, and have to go back from time to time when needed.

But basically, any sort of evolution that occurs in complex species also occurs in unicellular species. In addition, unicellular species are more open to horizontal transfer of genetic information. So evolution in unicellular species is less dependent on inherited DNA.

So, we do have unicellular species today. And I assume we can observe many generations of them within a reasonable period of time in experiment. So, do we see any unicellular species "evolved" in respond to controlled environmental changes?

 

[gluadys]

So, we do have unicellular species today. And I assume we can observe many generations of them within a reasonable period of time in experiment. So, do we see any unicellular species "evolved" in respond to controlled environmental changes?

Yes, here is one that has been running continuously since 1988.

http://myxo.css.msu.edu/ecoli/

Here is the Wikipedia description of this experiment

Lenski's long-term evolution experiment with Escherichia coli

On February 15, 1988, Richard Lenski started a long-term evolution experiment with the bacterium E. coli. The experiment continues to this day, and is by now probably the largest controlled evolution experiment ever undertaken. Since the inception of the experiment, the bacteria have grown for more than 40,000 generations. Lenski and colleagues regularly publish updates on the status of the experiments.​

 

[juvenissun]

Yes, here is one that has been running continuously since 1988.

http://myxo.css.msu.edu/ecoli/

Here is the Wikipedia description of this experiment

Lenski's long-term evolution experiment with Escherichia coli

On February 15, 1988, Richard Lenski started a long-term evolution experiment with the bacterium E. coli. The experiment continues to this day, and is by now probably the largest controlled evolution experiment ever undertaken. Since the inception of the experiment, the bacteria have grown for more than 40,000 generations. Lenski and colleagues regularly publish updates on the status of the experiments.​

Very good. However, I don't understand the data they presented. However, I guess that they have not seen the E. coli made any change significant enough to merit another name (?) for the bacteria. Is that true?

I use the word "name" because I do not know what does the "species" mean for a bacteria. It could be named differently, but would still be in that particular "species".

 

[gluadys]

Very good. However, I don't understand the data they presented. However, I guess that they have not seen the E. coli made any change significant enough to merit another name (?) for the bacteria. Is that true?

Not quite. They have observed the emergence of many different strains of E. coli--different variants. However, since bacteria are asexual reproducers they can't be tested for whether or not these are different "species" by trying to mate them.

As expected, all descendants of E. coli have the characteristics of E. coli, so there is no need to change the name.

I use the word "name" because I do not know what does the "species" mean for a bacteria. It could be named differently, but would still be in that particular "species".

With bacteria, and all species that reproduce asexually, "species" are defined by their morphological and behavioral characteristics. This, of course, was the original way all species were defined, but with obligate sexual reproduction, one can also use the criterion of whether or not they will freely mate with another population.

 

[juvenissun]

Not quite. They have observed the emergence of many different strains of E. coli--different variants. However, since bacteria are asexual reproducers they can't be tested for whether or not these are different "species" by trying to mate them.

As expected, all descendants of E. coli have the characteristics of E. coli, so there is no need to change the name.



With bacteria, and all species that reproduce asexually, "species" are defined by their morphological and behavioral characteristics. This, of course, was the original way all species were defined, but with obligate sexual reproduction, one can also use the criterion of whether or not they will freely mate with another population.

A quick search on Wikipedia gave me this:

E. coli is Gram-negative, facultative anaerobic and non-sporulating.

But I don't think this is the definition of E. coli. Could someone give me a formal and rigorous definition of E. coli?

Why does the experiment drag so long? Are they looking for a particular feature to happen? As I take a second look of the website, I feel the purpose of the project is to document how would E. coli change to different strains, but not to expect that E. coli will change to something which is not E. coli any more. At least I don't think it is an explicit goal.

 

[gluadys]

A quick search on Wikipedia gave me this:
But I don't think this is the definition of E. coli.

It is part of the definition. It gives you three of the characteristics of E. coli. The formal definition would include the characteristics that differentiate it from other gram-negative, facultative anaerobic, non-sporulating bacteria. It would take someone who is a microbiologist to list all the characteristics that identify E. coli.

Why does the experiment drag so long?

So they can observe long-term changes. Most experiments, due to limited funding, are more short-term. But you need long-term experiments to see long-term evolutionary change---like the 25 years the Grants spent observing Galapagos finches.

As I take a second look of the website, I feel the purpose of the project is to document how would E. coli change to different strains, but not to expect that E. coli will change to something which is not E. coli any more. At least I don't think it is an explicit goal.

Why would that be an explicit goal of an experiment in evolution?

 

[juvenissun]

It is part of the definition. It gives you three of the characteristics of E. coli. The formal definition would include the characteristics that differentiate it from other gram-negative, facultative anaerobic, non-sporulating bacteria. It would take someone who is a microbiologist to list all the characteristics that identify E. coli.




So they can observe long-term changes. Most experiments, due to limited funding, are more short-term. But you need long-term experiments to see long-term evolutionary change---like the 25 years the Grants spent observing Galapagos finches.




Why would that be an explicit goal of an experiment in evolution?

I don't think they expect (or worse, predict) that the E. coli would change to non-(E. coli). Even in a so-called evolution experiment, I bet this is not a goal listed in their proposal.

 

[juvenissun]

It is part of the definition. It gives you three of the characteristics of E. coli. The formal definition would include the characteristics that differentiate it from other gram-negative, facultative anaerobic, non-sporulating bacteria. It would take someone who is a microbiologist to list all the characteristics that identify E. coli.

I want to know what are those. So I can ask: why are they not changing?

 

[Melethiel]

I don't think they expect (or worse, predict) that the E. coli would change to non-(E. coli). Even in a so-called evolution experiment, I bet this is not a goal listed in their proposal.

As you've been told over and over again, evolution is built on a nested hierarchy. Thus, E. coli will ALWAYS be E. coli. When are you going to take the time to learn the fundamentals of evolutionary theory?

 

[juvenissun]

As you've been told over and over again, evolution is built on a nested hierarchy. Thus, E. coli will ALWAYS be E. coli. When are you going to take the time to learn the fundamentals of evolutionary theory?

I don't know much, but I am kind of agree with you. Evolution does not happen.

Seriously, I was not told about the idea of nested hierarchy at all. What is that? How is that applied to E. coli?

 

[gluadys]

I don't think they expect (or worse, predict) that the E. coli would change to non-(E. coli). Even in a so-called evolution experiment, I bet this is not a goal listed in their proposal.

I am quite sure it is not a goal listed in their proposal. And that is logical. Why would you think it logical to include such a goal? Why do you use the phrase "even in a so-called evolution experiment" as if a real evolution experiment would necessarily include that goal?

Do you think that they are not really observing evolution? Or not expecting to observe evolution?

Why?

 

[gluadys]

I don't know much, but I am kind of agree with you. Evolution does not happen.

Mallon is not saying that evolution does not happen. Evolution does happen. At least what biologists mean by evolution happens.

Now what you mean by evolution--that can be a different story. You have ideas about evolution that are not part of science. So it is quite likely that evolution--as you think of it---does not happen.

But as biologists describe it, yes, evolution happens.

What evolution produces through history is a nested hierarchy of groups within groups within groups.

This is fundamental to any understanding of evolution.

It is the reason the researchers in the E. coli experiment do not expect the various strains to be something other than E. coli.

It is the reason all those experiments on fruit flies are not expected to produce something other than fruit flies.

Did you see the post of JimLarmore on cytochrome c divergence? (In the mitochondrial DNA thread). The nested hierarchy is the reason those numbers are supposed to be the same--why they are supportive evidence of evolution, not an argument against it.

Seriously, I was not told about the idea of nested hierarchy at all. What is that?

Really? It is so basic, I am surprised we missed speaking to you about it. Here is an explanation (quite short and readable, so please take a look at it.)

http://locolobo.org/Taxonomy.html

How is that applied to E. coli?

E. coli is one twig on the tip of a branch of the tree. (The nested hierarchy is often presented as a tree--like a family tree.) As it evolves, it will produce new twigs and leaves, but all of them will be E. coli too.

 

[juvenissun]

Did you see the post of JimLarmore on cytochrome c divergence? (In the mitochondrial DNA thread). The nested hierarchy is the reason those numbers are supposed to be the same--why they are supportive evidence of evolution, not an argument against it.

Really? It is so basic, I am surprised we missed speaking to you about it. Here is an explanation (quite short and readable, so please take a look at it.)

http://locolobo.org/Taxonomy.html

OK. Thanks. It is just the term. I think I know the idea.

Yes. I read posts with rich content carefully, in fact, word by word. I want to learn more on this aspect when I can.

 

[juvenissun]

I am quite sure it is not a goal listed in their proposal. And that is logical. Why would you think it logical to include such a goal? Why do you use the phrase "even in a so-called evolution experiment" as if a real evolution experiment would necessarily include that goal?

Do you think that they are not really observing evolution? Or not expecting to observe evolution?

Why?

IF, I were an evolutionist, I WILL devote my whole effort to prove that evolution does happen. Not only we see "change", but it changes to such an extent that we see speciation (however is it defined). So, with that purpose, I will explicitly say in the proposal that I like to see the E. coli evolves into something else (based on some reasons, of course).

The word evolution in that research title is misleading, or confusing, at least.