9 Questions

[J_B_]

Interesting questions. Based on what little I know of the subject, I would think the answer to both questions would be no. They would have to be very similar to known critters. We're still a long way from figuring out everything that goes into DNA.

What is your background? At some point I hope one of the resident biologists responds.

 

[Tanj]

What is your background? At some point I hope one of the resident biologists responds.

Why would we respond to a philosophical question? We're biologists, not philosophers. We're waiting for an actual biological question.

 

[Yttrium]

What is your background? At some point I hope one of the resident biologists responds.

BS Physics, MS Math. I've only had two college classes in biology.

 

[J_B_]

Why would we respond to a philosophical question? We're biologists, not philosophers. We're waiting for an actual biological question.

I can't respond to that without getting philosophical, so check out post #56.

 

[durangodawood]

Why would we respond to a philosophical question? We're biologists, not philosophers. We're waiting for an actual biological question.

Speak for yourself.

I love playing internet philosopher. And I've got all the credentials required.

 

[Astrophile]

I tried to be clear that I wasn't speaking to a complete lack of evidence, but let me try to elaborate further.

Theory AAA is currently the only explaination for the formation of 111 objects. Not all of these objects are identical. Objects 111a, 111b, 111c, etc. have been observed. There is evidence for the formation of 111a, 111b, and 111c per the mechanisms of theory AAA. A new object is observed (111d), but there is not yet any evidence of its formation.

Is theory AAA sufficient explanation for 111d without that evidence?

Not necessarily. To take the example of star formation, most stars probably form by the collapse and fragmentation of the cores of relatively dense interstellar clouds. However, it has been proposed that the most massive O-type stars and blue stragglers in star cluster form by the mergers of binary stars, so that the theory of interstellar cloud collapse would not necessarily apply to these stars without evidence.

 

[J_B_]

Not necessarily. To take the example of star formation, most stars probably form by the collapse and fragmentation of the cores of relatively dense interstellar clouds. However, it has been proposed that the most massive O-type stars and blue stragglers in star cluster form by the mergers of binary stars, so that the theory of interstellar cloud collapse would not necessarily apply to these stars without evidence.

In that case you have a 2nd theory (or is it a hypothesis?). Regardless, great example.

 

[lsume]

I wouldn't call any idea a "scientific theory" that is without evidence. Hypothesis, maybe.

Postulate

 

[Occams Barber]

I have 9 questions about evolution. I understand they have the potential for heated conversation, but I’m hoping to fill some gaps in my knowledge. I will do my best to remain civil. As we proceed, some questions may become moot, or the conversation may prompt new questions. However, at the moment I have 9.

Just to be clear, I’m using the following as a definition of evolution: A change in allele frequency of a population from one generation to the next.

Given that is the definition, it is obvious evolution happens, so the questions are not aimed at whether or not it happens, but at how biologists characterize, analyze, and predict the objects and phenomena that make up evolution.

Question #1: If there is only one scientific theory explaining a phenomenon, is that theory a sufficient explanation for an occurrence of the phenomenon even without evidence?

This is a philosophical question. I am aware of the evidential claims for evolution, so I don’t need them repeated. I’m just looking for an answer to the philosophical question.

[edit]: Questions 2/3 are posted here.

Hello JB
I've been following the conversation with some interest. I've noticed that a few posters have responded to you with a somewhat guarded tone and I thought you might be interested in understanding why this is so.

I've been around CF for close on ten years. In that time I've seen a variety of Creationist approaches to the Creation/Evolution debate.

One common tactic is to pose as a reasonable and rational Christian who's a little confused about Evolution. Having established his credentials as a Good Guy he then proceeds to ask disingenuous questions which contain (in his view) hidden 'Gotcha' hooks aimed at tripping up the Evolutionists and 'proving' Creationism. Typically it becomes very obvious that said Creationist doesn't understand Evolution and what he thought was a mind blowing truth is actually some PRATT which has been around the block many times. It usually ends with the Creationist storming off in a fit of pique when it's pointed out that they are woefully under equipped for the discussion.

Why am I telling you this?

I'm sure you're not one of these 'Good Guys' but your approach creates the impression that you may be. The result is that you will be regarded with some suspicion. For instance, we have no idea of the overall point of your questions and none of your three questions so far are about evolution. Q1 is about the nature of a theory, while Qs 2 & 3 are about links between DNA and morphology.

Why not be upfront instead? Put your cards on the table and make it clear you are genuinely interested in a discussion?

What's the point of your nine questions?

OB

 

[That Guy 11200]

Though the first question was philosophical, the remaining 8 are specific to evolution. Sorry if that disappoints anyone.

I'm tagging everyone who replied to the first question. If you don't want me to do that for the remainder of the questions, just let me know: @Tinker Grey @durangodawood @Yttrium @Estrid @Frank Robert @essentialsaltes @FrumiousBandersnatch

Question #2: Given a DNA sequence, is there currently a means (based on the DNA alone) for determining if that sequence will produce a viable organism and what the morphology of that organism will be?

We know of several genes that appear to be essential to life. If they aren't part of the sequence, then it wouldn't be a viable organism. But experiments are ongoing to test whether it's actually the case that all of these genes are essential.

Also, in animals, mutations often occur in gamete genes that prevent fetuses developing. A large proportion of conceptions fail in the first few days. I imagine there would be too many variations to keep track of individually.

You also have to consider that whole genome sequencing is relatively new, and there are a lot of genes in nature that would have to be selectively switched off/on, in organisms to determine what they do.

So, at the moment, not so much, but possibly one day it will be possible.

Question #3: Given the morphology of an organism, is there currently a means (based on morphology alone) for determining its DNA?

No. Morphology is affected by the environment, food and epigenetics (chemicals that affect which genes are 'switched on' in an organism), not just an organism's DNA. Also, not all genes (more accurately, the proteins those genes are a template for) affect morphology and genes are only part of a DNA sequence, a lot of it is 'non-coding'. So, not all DNA is used to make the proteins that affect morphology and, therefore, it would be impossible to determine a DNA sequence from morphology.

 

[FrumiousBandersnatch]

Question #2: Given a DNA sequence, is there currently a means (based on the DNA alone) for determining if that sequence will produce a viable organism and what the morphology of that organism will be?

I doubt it. It is possible to determine specific sequences that are non-viable, and specific sequences that influence morphology, but DNA is not a blueprint, it is more like a recipe. An organism doesn't develop in a void - environmental conditions during development are important.

Question #3:

Given the morphology of an organism, is there currently a means (based on morphology alone) for determining its DNA?

No. Again, there are some features that will correlate to specific sequences, but unless you already know the correlations between DNA and morphology for that species, it would be highly speculative. Knowing the DNA and morphology correlations of similar species would allow you to make informed guesses at some of it.

 

[Estrid]

What is your background? At some point I hope one of the resident biologists responds.

There is a saying, you have to know most of the answer before you
can ask a good question.

 

[J_B_]

Hello JB
I've been following the conversation with some interest. I've noticed that a few posters have responded to you with a somewhat guarded tone and I thought you might be interested in understanding why this is so.

I've been around CF for close on ten years. In that time I've seen a variety of Creationist approaches to the Creation/Evolution debate.

One common tactic is to pose as a reasonable and rational Christian who's a little confused about Evolution. Having established his credentials as a Good Guy he then proceeds to ask disingenuous questions which contain (in his view) hidden 'Gotcha' hooks aimed at tripping up the Evolutionists and 'proving' Creationism. Typically it becomes very obvious that said Creationist doesn't understand Evolution and what he thought was a mind blowing truth is actually some PRATT which has been around the block many times. It usually ends with the Creationist storming off in a fit of pique when it's pointed out that they are woefully under equipped for the discussion.

Why am I telling you this?

I'm sure you're not one of these 'Good Guys' but your approach creates the impression that you may be. The result is that you will be regarded with some suspicion. For instance, we have no idea of the overall point of your questions and none of your three questions so far are about evolution. Q1 is about the nature of a theory, while Qs 2 & 3 are about links between DNA and morphology.

Why not be upfront instead? Put your cards on the table and make it clear you are genuinely interested in a discussion?

What's the point of your nine questions?

OB

The forum is full of jaded people on both sides, and that does make it difficult to have an open conversation. Since high school (early 1980s) I've never been interested in biology for biology's sake. My dad forced me to take biology (which was probably good), when I much preferred physics. Yet, also since high school, people around me have been engaged in fights over evolution. As such, people-watching and the philosophy of science is what interests me much more than the subject matter. However, in order to participate in the conversation in a meaningful way, I need to understand the debate. I've tried to educate myself.

Several decades ago I did think I had a unique perspective on evolution ... well, I probably still do think that ... but in the past I thought my unique view was clever. I don't think that anymore. Part of educating myself was having serious sit down discussions with biologists ... and now I'm here, which indicates how that went. If I thought my ideas were unusually clever, I wouldn't be posting them here. I'd be developing a paper for publication.

My purpose is as I stated it - to fill the gaps in my knowledge. These questions came up. I don't know the answers, and I don't recall seeing it discussed here before. If all of this has been run through the mill multiple times, it should be easy to dispose of it.

You're going to be disappointed about my purposes at the end, because when the 9 questions are done, I plan to shut down the thread and move on. People always ask my motivations with great suspicion. In the past I used to share some of my thoughts about evolution, but all that leads to is, "Aha! I knew you were a devious creationist with evil motives! Gotcha!" I don't need that, so I don't share anymore. @durangodawood did indicate an interest in a further philosophy of science discussion. A philosophy of biology thread could be a fun chat with him, because he seems sincere, but that's for another time and place.

 

[J_B_]

We know of several genes that appear to be essential to life. If they aren't part of the sequence, then it wouldn't be a viable organism. But experiments are ongoing to test whether it's actually the case that all of these genes are essential.

Cool. I didn't know that.

My engineering experience has been that if I think of something, someone else already thought of it before me. Given I'm not a biologist, I assume it's only more so the case in biology. However, when you don't know what you don't know ...

No. Morphology is affected by the environment, food and epigenetics (chemicals that affect which genes are 'switched on' in an organism), not just an organism's DNA. Also, not all genes (more accurately, the proteins those genes are a template for) affect morphology and genes are only part of a DNA sequence, a lot of it is 'non-coding'. So, not all DNA is used to make the proteins that affect morphology and, therefore, it would be impossible to determine a DNA sequence from morphology.

Sure. I was aware environment can affect morphology. Maybe my question was a bit clumsy, as I meant prediction of a morphology unaffected by environment. However, I see now how that would be tough to square with organisms who are always living in an environment.

Thanks for the answers.

 

[J_B_]

I doubt it. It is possible to determine specific sequences that are non-viable, and specific sequences that influence morphology, but DNA is not a blueprint, it is more like a recipe. An organism doesn't develop in a void - environmental conditions during development are important.

No. Again, there are some features that will correlate to specific sequences, but unless you already know the correlations between DNA and morphology for that species, it would be highly speculative. Knowing the DNA and morphology correlations of similar species would allow you to make informed guesses at some of it.

That's what I suspected - that it's based on comparisons of known DNA-morphology sets rather than an ability to model a direct link. However, I'd think some are trying to establish that direct link? Maybe? I don't know of anyone trying to establish direct links from material science to mechanics for my field, and in my opinion it seems a near impossible thing to do, but maybe some in biology are giving it a go.

On the other side, I know there is Stuart Kaufmann's camp that is saying biology is emergent, and therefore the link is impossible.

 

[J_B_]

There is a saying, you have to know most of the answer before you can ask a good question.

That's an interesting saying. If it's true those of use seeking new knowledge are doomed, though I've never been afraid of bootstrapping and having people call me stupid in the process. The results I get satisfy me more than the barbs of the detractors.

I think of it more in terms of serendipity. Even people with experience need to guess or get lucky from time to time, but their experience is still valuable because they can identify a good result when it happens. Managers in my line of work are always coming up with clever schemes where the uninitiated will supposedly be more successful than an experienced engineer such as myself. Brainstorming teams where we were forced to try the ideas of people with no experience. Big data projects where engineers were not supposed to give input. All kinds of wonderful schemes. It's not worked so far, though they continue to grasp for those lower costs.

I'm all for having inexperienced people on my team because I enjoy helping them learn. But having them lead. Yeah, that's a stupid idea.

 

[J_B_]

Question #4: For any given path through a phylogenetic tree, how many generations have passed from a progenitor species to the current species? For example, from Juramaia to Sylvilagus? (feel free to pick another example - maybe the best documented one you are aware of)

Question #5: For that series of generations how many have an extant specimen (living, preserved, remains, fossil, etc.)?

Question #6: Of the extant specimens, how many come as a DNA-morphology set?

@Tinker Grey @durangodawood @Yttrium @Estrid @Frank Robert @essentialsaltes @FrumiousBandersnatch @Astrophile @That Guy 11200

 

[Estrid]

Hello JB
I've been following the conversation with some interest. I've noticed that a few posters have responded to you with a somewhat guarded tone and I thought you might be interested in understanding why this is so.

I've been around CF for close on ten years. In that time I've seen a variety of Creationist approaches to the Creation/Evolution debate.

One common tactic is to pose as a reasonable and rational Christian who's a little confused about Evolution. Having established his credentials as a Good Guy he then proceeds to ask disingenuous questions which contain (in his view) hidden 'Gotcha' hooks aimed at tripping up the Evolutionists and 'proving' Creationism. Typically it becomes very obvious that said Creationist doesn't understand Evolution and what he thought was a mind blowing truth is actually some PRATT which has been around the block many times. It usually ends with the Creationist storming off in a fit of pique when it's pointed out that they are woefully under equipped for the discussion.

Why am I telling you this?

I'm sure you're not one of these 'Good Guys' but your approach creates the impression that you may be. The result is that you will be regarded with some suspicion. For instance, we have no idea of the overall point of your questions and none of your three questions so far are about evolution. Q1 is about the nature of a theory, while Qs 2 & 3 are about links between DNA and morphology.

Why not be upfront instead? Put your cards on the table and make it clear you are genuinely interested in a discussion?

What's the point of your nine questions?

OB

The mention of "bias" is usually a tell.

 

[Estrid]

That's an interesting saying. If it's true those of use seeking new knowledge are doomed, though I've never been afraid of bootstrapping and having people call me stupid in the process. The results I get satisfy me more than the barbs of the detractors.

I think of it more in terms of serendipity. Even people with experience need to guess or get lucky from time to time, but their experience is still valuable because they can identify a good result when it happens. Managers in my line of work are always coming up with clever schemes where the uninitiated will supposedly be more successful than an experienced engineer such as myself. Brainstorming teams where we were forced to try the ideas of people with no experience. Big data projects where engineers were not supposed to give input. All kinds of wonderful schemes. It's not worked so far, though they continue to grasp for those lower costs.

I'm all for having inexperienced people on my team because I enjoy helping them learn. But having them lead. Yeah, that's a stupid idea.

All of that BUT.
People routinely go on forums and ask (" ask")
idiotic questions reflecting less than zero knowledge
of the subject, generally hoping for a gotcha with
some supposed zinger picked up from a preacher
or creosite.

If doom is an issue at all, then its that we ate doomed
to see this so- familiar pattern repeated.

And the false seekers are among other things doomed
to be told to come to the table better prepared.

Perhaps you have shared my experience, at a board
meeting having someone chirp a stupid question
that showed total lack of preparation.

If so you'd see the sense of what I said, see if it applies
and not waste our time trying to refute it.

 

[Hans Blaster]

Question #2: Given a DNA sequence, is there currently a means (based on the DNA alone) for determining if that sequence will produce a viable organism and what the morphology of that organism will be?

No. And there may never be.

If we know a gene (a segment of DNA) encodes a protein, we do know what amino acids the protein will be made of (and in what order). I think we can replicate the protein in the lab from the sequence. Computing the shape of the protein from just the sequence is something that is being worked on. (There are some difficulties, but significant progress is being made.)

Even if we identify all of the protein encoding genes in a genome, computationally replicate them, and determine how they interact with each other we are only part way to understanding (from scratch) the function of a single cell.

Not all proteins are expressed in every cell at all times. There are regulatory parts of the genome. There is the feedback on the gene expression from within the cell. There are the non-protein parts of the cell, etc.

Even if we could work out what one cell is doing (for example if we could reconstruct a single-celled organism from its DNA alone), we would still have to work out how the organism grew, its organs formed ,etc.