Evolution- inspire me~ please!

[rossum]

The theory of evolution presupposes a one-celled or extremely simple lifeform as the beginning of life in the universe.

No, as the beginning of life on earth. We do not have enough information about life elsewhere in the universe yet.

Where does this life-form come from?

As you said in your previous post, we are working on it. Abiogenesis is far less well understood than evolution.

Scientifically, there is no explanation. Is that what you are saying?

The default position in science is “we don’t know”. Abiogenesis is not quite that bad, but it is close to it, say “we don’t know much so far”.

If so, IMO that takes credibility away from evolutionary theory. If your presupposition is invalid, then your theory is invalid, or at the very least, highly questionable…

It is neither invalid nor highly questionable. Twenty billion years ago there was no life on earth. Today there is life on earth, therefore life on earth must have originated sometime in the last twenty billion years. We cannot yet say precisely how it originated, but at some point it must have done so. Evolution starts from there. If it were proved that God really did breathe life into that first organism then there would be no changes at all to the theory of evolution. Abiogenesis would change out of all recognition of course, but evolution would be unaffected.

Chemistry does not explain the orign of the elements, it just assumes that they exist and takes it from there. Are you saying that chemistry is invalid? A different theory - stellar physics - explains the origin of the elements. Similarly evolution and abiogenesis divide the work between them. Abiogenesis gets us from a lifeless earth to an earth with one primitive living cell. Evolution gets us from that one cell to what we have now. Even without knowing all the details of abiogenesis we can know that it happened somehow. If it didn’t then we wouldn’t be here.

Can you name your great ^ 27 grandfather? What was his name? Where did he live? What did he do? How old was he when he died? You know nothing about him, yet you know that he must have existed because you are here now.

rossum

 

[ricmat]

I disagree.
Natural selection is about differential reproductive success - getting more copies of your genes into subsequent generations. It is an average process; as you say one copy of a beneficial mutation might get eaten but then the next time that mutation happens it might survive, and overall it has less chance of being eaten than an unmutated organism because we are looking at a beneficial mutation.

But if there is no killing off due to natural selection, then that means that the beneficial mutations all survive. And with no natural selection in the model, there are no such things as competing for limited resources. So they all reproduce, including the beneficial mutations, in an unlimited fashion. You’d have even more organisms with the beneficial mutations than you do when you include natural selection. I don’t think this “lack of natural selection” hurts your probability.

The mutation rate for mammals is about 3 x 10[sup]-8[/sup] mutations per base pair per generation. Applying this rate to humans we would expect about 100 mutations in the 3.2 x 10[sup]9[/sup] base pairs of the human genome. With six billion individuals in the human population this is 600 billion individual mutations over the whole human population in each generation. If a beneficial mutation does not take the first time around there will be another one along shortly.

You are wrong on this. In my Boojumase model I compare the random probability (tornado in a junkyard model) with a more complex model including natural selection. The time taken to evolve a 100 amino acid protein is 6.35 x 10[sup]130[/sup] years on the random model and 2.1 million years on the model including natural selection. That is a major difference and moves the scenario from highly unlikely to perfectly possible in the time available.

rossum

So if the 100 amino acid protein takes only 2.1 million years (I’ll assume for the moment that it is correct), how long does it take to go from simple life to complex life?

Another question. (Sorry if you’ve covered this previously…) This has to do with your previous mention of the relative rates of beneficial, neutral, and harmful mutations. I’m obviously not an expert on this, so I’m asking what I think are common sense questions. I find it difficult to believe that most mutations are “neutral” which I think you said previously, instead of harmful (at least for complex creatures). Human DNA could be thought of as a string of (billions? trillions? zillions?) of beneficial mutations that happened in sequence. And any “random” mutation that comes along has a much greater risk of breaking something that works rather than creating some sort of improvement.

By analogy, a fully functional software program with trillions (or even hundreds) of lines of code is easy to make partially cripple, or totally useless (like the blue screen of death) by randomly changing one line of code. And I have yet to see any improvements made by randomly adding or changing lines of code. Now I do admit that if you have no program at all, or even a very simple program with only a few lines of code, that randomly adding and changing the code might lead to a different program that does something. But when you get past just a few lines, this idea falls apart, for me at least.

 

[buffalo]

I found this to be cool -

The Richard Dawkins Mutation Challenge

Anybody try this yet?

 

[rusty20]

But if there is no killing off due to natural selection, then that means that the beneficial mutations all survive. And with no natural selection in the model, there are no such things as competing for limited resources. So they all reproduce, including the beneficial mutations, in an unlimited fashion. You’d have even more organisms with the beneficial mutations than you do when you include natural selection. I don’t think this “lack of natural selection” hurts your probability.

So if the 100 amino acid protein takes only 2.1 million years (I’ll assume for the moment that it is correct), how long does it take to go from simple life to complex life?

Another question. (Sorry if you’ve covered this previously…) This has to do with your previous mention of the relative rates of beneficial, neutral, and harmful mutations. I’m obviously not an expert on this, so I’m asking what I think are common sense questions. I find it difficult to believe that most mutations are “neutral” which I think you said previously, instead of harmful (at least for complex creatures). Human DNA could be thought of as a string of (billions? trillions? zillions?) of beneficial mutations that happened in sequence. And any “random” mutation that comes along has a much greater risk of breaking something that works rather than creating some sort of improvement.

By analogy, a fully functional software program with trillions (or even hundreds) of lines of code is easy to make partially cripple, or totally useless (like the blue screen of death) by randomly changing one line of code. And I have yet to see any improvements made by randomly adding or changing lines of code. Now I do admit that if you have no program at all, or even a very simple program with only a few lines of code, that randomly adding and changing the code might lead to a different program that does something. But when you get past just a few lines, this idea falls apart, for me at least.

just want to say, good points

 

[rusty20]

No, as the beginning of life on earth. We do not have enough information about life elsewhere in the universe yet.

As you said in your previous post, we are working on it. Abiogenesis is far less well understood than evolution.

The default position in science is “we don’t know”. Abiogenesis is not quite that bad, but it is close to it, say “we don’t know much so far”.

So, you basically admit that science has no clear idea of how life may have arisen from a pool of chemicals? Perhaps this is because the origin of life is not scientific in nature.

It is neither invalid nor highly questionable. Twenty billion years ago there was no life on earth. Today there is life on earth, therefore life on earth must have originated sometime in the last twenty billion years. We cannot yet say precisely how it originated, but at some point it must have done so. Evolution starts from there. If it were proved that God really did breathe life into that first organism then there would be no changes at all to the theory of evolution. Abiogenesis would change out of all recognition of course, but evolution would be unaffected.

rossum

My problem with this is that evolution rests on random (beneficial - which is extremely rare) mutation and natural selection. You seemingly discounted my probabilities quoted from a source earlier. Would you be so kind as to provide a source showing the ‘correct’ probabilities of evolutionary theory? Like the probability of random beneficial mutation? Anything of this nature?

My apologies if you have already done so in this thread…

 

[rossum]

But if there is no killing off due to natural selection, then that means that the beneficial mutations all survive.

My apologies for not expressing myself more clearly. On average a beneficial mutation will result in more copies of itself being passed on into the next generation. It is on average over the whole population. Individual animals with the mutation may fail to reproduce, but on average animals with the mutation will have more offspring than those without.

And with no natural selection in the model, there are no such things as competing for limited resources.

Better to put that the other way round. If there are unlimited resources then natural selection is absent.

So if the 100 amino acid protein takes only 2.1 million years (I’ll assume for the moment that it is correct), how long does it take to go from simple life to complex life?

Pass. You need to define “simple” and “complex”. To get from the origin of life on earth to now took about four billion years.

I find it difficult to believe that most mutations are “neutral” which I think you said previously, instead of harmful (at least for complex creatures).

Most mutations are indeed neutral. Firstly there are synonymous mutations. The genetic code uses 64 codons to code for 20 amino acids, so each amino acid generally has more than one codon. For example Proline (Pro/P) has four codons: CCT, CCC, CCA, CCG. Hence a mutation from CCT to CCA will not change the amino acid coded for. Secondly a lot of human DNA does not actually code for anything (often called “junk DNA”), for example introns. Thirdly, not all changes to proteins have any real effect. Proteins tend to be made up of active areas (where changes do have a big effect) and non-active areas which can take quite a lot of changes without affecting the function of the protein. Fourthly, not all changes are significant: it is not clear that eye colour in humans actually has any real effect, either beneficial or deleterious.

In general about 95% of mutations in humans are neutral. We average about 100 mutations each, only five of which have any real effect. Almost always the five are deleterious.

You are correct that the vast majority of non-neutral mutations are deleterious. If something is well adjusted for its environment then random changes are unlikely to be good. However since the environment is changing we are not perfectly adjusted to it so there is a small gap for the occasional beneficial mutation. For example, our diet in the west has changed to include a lot more fats which gives an opportunity for a mutation to improve the way we deal with fats in our bloodstream: A Rare Protein Mutation Offers new Hope for Heart Disease Patients

Human DNA could be thought of as a string of (billions? trillions? zillions?) of beneficial mutations that happened in sequence. And any “random” mutation that comes along has a much greater risk of breaking something that works rather than creating some sort of improvement.

There are trillions of different ways to make a human being, remember that DNA testing can easily identify individuals. Even within a single protein there are many ways of making it, any one of which will work. For instance it has been calculated that there are 2 x 10[sup]93[/sup] ways to make Cytochrome C (Yockey 1992). Evolution is not searching for a single target, but for any one of a large number of possible targets.

Remember that there is a very severe constraint on any population: every ancestor of every individual in the population succeeded in reproducing. Your “breaking” happens a lot, and those individuals either fail to reproduce, or reproduce at a lesser rate. Either way the breaks are eliminated from the population.

By analogy, a fully functional software program with trillions (or even hundreds) of lines of code is easy to make partially cripple, or totally useless (like the blue screen of death) by randomly changing one line of code.

DNA code has no equivalent of the BSoD: all base sequences will produce some sort of protein, except for the sequence start-stop which produces nothing, but still does not break the system. Any computer simulation of evolution needs to be set up to reflect this, the program (protein) may not do anything useful but it will never crash the system.

Read Lenski et. al. The Evolutionary Origin of Complex Features for an example of what a more realistic computer simulation of evolution can do.

rossum

 

[rossum]

So, you basically admit that science has no clear idea of how life may have arisen from a pool of chemicals? Perhaps this is because the origin of life is not scientific in nature.

I have never seen a non-scientific chemical. You are in danger of putting forward a God of the gaps argument here. Generally all that does is make your God vulnerable to science. “We are to find God in what we know, not in what we do not know; God wants us to realize his presence, not in unsolved problems but in those that are solved.” - Dietrich Bonhoeffer.

My problem with this is that evolution rests on random (beneficial - which is extremely rare) mutation and natural selection. You seemingly discounted my probabilities quoted from a source earlier. Would you be so kind as to provide a source showing the ‘correct’ probabilities of evolutionary theory? Like the probability of random beneficial mutation? Anything of this nature?

The probability of a beneficial mutation depends on how well the organism is adapted to its environment. If the organism is well adapted then there is a very small space for beneficial mutations. If the organism is less well adapted - maybe it has just moved to a new area or the place it is living has changed - then there is more of a chance for a beneficial mutation.

For example cave fish do not need eyes, so mutations that prevent wasting resources building eyes are beneficial to them. Fish living outside the caves would find those mutations deleterious.

rossum

 

[rusty20]

The probability of a beneficial mutation depends on how well the organism is adapted to its environment. If the organism is well adapted then there is a very small space for beneficial mutations. If the organism is less well adapted - maybe it has just moved to a new area or the place it is living has changed - then there is more of a chance for a beneficial mutation.

rossum

You are talking about adaptation, or microevolution, not macroevolution. This is like saying dogs raised in alaska will tend to grow thicker hair over generations. This kind of mutation is an animal adapting to its environment, this is NOT evolution. Evolution takes this easily observable action, and expands it to attempt to explain the abundance of varying lifeforms on the planet.

Either way, you have failed to provide a source of any probability regarding evolution. Perhaps you could provide two different probabilities then, one for an animal in a perfect environment, and one in an environment detrimental to its survival?

 

[rossum]

You are talking about adaptation, or microevolution, not macroevolution.

Evolution can be defined as “change in the genomes of a population over time”. Microevolution is defined as “changes below the level of species”. Macroevolution is defined as “changes at or above the level of species”. Some creationists use the terms macroevolution and microevolution differently, referring to ‘kind’ rather than species.

All the mechanisms of microevolution also apply to macroevolution, with some extra mechanisms such as geographical separation being added for macroevolution. The smallest amount of genetic change I am aware of that causes macroevolution (a new species) is three mutations. One mutation caused a change in colouration and the two others changed the time of breeding. Three mutations is not a difficult thing to envisage. For other examples of macroevolution see Observed Instances of Speciation, Some More Observed Speciation Events and 29+ Evidences for Macroevolution.

This is like saying dogs raised in alaska will tend to grow thicker hair over generations. This kind of mutation is an animal adapting to its environment, this is NOT evolution.

Yes it is evolution. You can call it microevolution if you like but it is still evolution. The genomes of that population of dogs are changing over time.

Evolution takes this easily observable action, and expands it to attempt to explain the abundance of varying lifeforms on the planet.

Correct. It does and it has been seen to do so. I gave the links above.

Either way, you have failed to provide a source of any probability regarding evolution.

I do not have enough detail to provide a worthwhile calculation. You have to define precisely the environment the population is living in and exactly how closely the genomes of that population reflect that environment. Remember that beneficial, neutral or deleterious can depend on the environment.

Perhaps you could provide two different probabilities then, one for an animal in a perfect environment, and one in an environment detrimental to its survival?

If an organism is perfectly adapted to its envorinment then it will not have any beneficial mutations, since it is already perfectly adapted. All mutations would either be neutral or deleterious. However, since all environments change over time this perfect adaptation cannot last for ever.

In a situation where the organism is not well adapted to its environment - say a large meteorite strike has changed the environment drastically overnight - then there are two possibilities. Either the organism is so maladapted that it will go extinct, or else it is badly adapted, but not too badly adapted, so it can survive and will have a relatively large scope for beneficial mutations. When the Chicxulub meteorite hit the dinosaurs were in the first category while the birds and mammals were in the second. The basic criterion for survival seems to have been size, all reasonably large land animals went extinct. All the survivors were small, something about cat-sized or a small dog was the biggest that survived.

rossum

 

[CThomas]

Okay, Rossum, I’m back. I once again wanted to belatedly follow up on your response to my question (numbered 29 in this discussion series). There you say: “Some of our genes have enough variation to indicate that the latest possible date for a bottleneck as narrow as one breeding pair was two million years ago.” Another dumb question: Why isn’t that perfectly consistent with the Genesis story? Doesn’t our current scientific knowledge peg the human species as beginning somewhere around 2-3 million years ago? If so, then why is the 2-million year period for the earlier bottleneck not wholly consistent with the Genesis account?

Thanks, and regards.

CThomas

 

[rossum]

Okay, Rossum, I’m back. I once again wanted to belatedly follow up on your response to my question (numbered 29 in this discussion series). There you say: “Some of our genes have enough variation to indicate that the latest possible date for a bottleneck as narrow as one breeding pair was two million years ago.” Another dumb question: Why isn’t that perfectly consistent with the Genesis story?

It is consistent with some interpretations of Genesis, not with others.

Doesn’t our current scientific knowledge peg the human species as beginning somewhere around 2-3 million years ago?

No, Homo sapiens is about 150,000 to 200,000 years old as a species. Before that our ancestors were not Homo sapiens but something else. At 2 million years ago our ancestors would have been Homo erectus or similar. At 3 million years ago our ancestors were not even in genus Homo but Australopithecus.

If so, then why is the 2-million year period for the earlier bottleneck not wholly consistent with the Genesis account?

That depends on the interpretation of Genesis that you are using. What species was Adam? Is the YEC style 6,000 year timescale correct or not? There are many possible interpretations of Genesis. To quote Aquinas:“In discussing questions of this kind two rules are to be observed, as Augustine teaches. The first is, to hold to the truth of Scripture without wavering. The second is that since Holy Scripture can be explained in a multiplicity of senses, one should adhere to a particular explanation only in such measure as to be ready to abandon it if it be proved with certainty to be false, lest Holy Scripture be exposed to the ridicule of unbelievers, and obstacles be placed to their believing.”
Wise advice.

rossum

 

[buffalo]

Anybody try this yet?

No takers? What are you afraid of? Nobody can beat Dawkins?

The Richard Dawkins Mutation Challenge

 

[CThomas]

Thanks, Rossum. To be clear, I’m operating under the day-age construction, and I’m just trying to clarify in my own mind what you view as the constraints imposed upon the available textual readings of Genesis. Based on my limited knowledge, I see no special reason why the biblcal account of humanity could not begin with organisms that we would today classify as homo erectus. Clearly nothing in the biblical Hebrew could be read to draw these sorts of modern species classifications.

Regards,

CThomas

 

[rossum]

Thanks, Rossum. To be clear, I’m operating under the day-age construction, and I’m just trying to clarify in my own mind what you view as the constraints imposed upon the available textual readings of Genesis.

I am Buddhist, so I am reluctant to tell any Christian how they should interpret Genesis. I generally comment on science rather than scriptures. From the point of view of science we can say:* souls do not fossilise and they do not appear in our DNA so we can say nothing about them.

• the human (Homo sapiens) population has never been as low as a single pair, or as low as four pairs as with a worldwide interpretation of the Noahic flood.
• our material bodies show all the signs of having evolved from earlier upright apes: earlier Homo and before that Australopithecus.
• we are primates, and have been classified as primates since 1735.

On the point of population sizes, that is the size of the population of physically human upright apes. Science can tell us nothing of how many of those apes had souls and how many did not.

Based on my limited knowledge, I see no special reason why the biblcal account of humanity could not begin with organisms that we would today classify as homo erectus. Clearly nothing in the biblical Hebrew could be read to draw these sorts of modern species classifications.

Agreed. The Bible classifies bats and birds together, which is not how modern biology classifies them. The Bible is not a science textbook.

rossum

 

[Jennifer_G]

Here’s how I view Genesis -

Day and night I think are more of a metaphore (more like an era - 1-2 billion years maybe). The first day was there even before the Earth was formed. The very, very first thing that came into existance in the universe was light (scientists say that if you have a telescope powerful enough, and look far enough, you can see a huge wall of light).

God let all of his creatures (save for angels for the most part) have free will, so a creature can choose to start eating plants, or other animals or whatnot, and over time, the creature changes its’ appearance to fit their environment. When it came to man-like creatures, the way I always looked at it (and I think the pope recently mentioned something to that effect - I read it in an article somewhere) was that the first man was when God gave man a soul, and extra spark that created the first real man.

As for dinosaurs, etc., here’s a summary of what I read on the EWTN’s Q&A site - when God created all of the creatures of the Earth (Day 5 I think?), dinosaurs were included, as well as all other creatures that ever lived.

One thing to remember is that, we operate with a sense of time. We only live in 1 dimension of time (think of a timeline). We only know of now, and know what happened in the past, but can’t see the future. God is outside of time (what would that be? 4 dimensions of time? ), so time is irrelevant, since it has already happened from that viewpoint.

 

[buffalo]

Here’s how I view Genesis -

Day and night I think are more of a metaphore (more like an era - 1-2 billion years maybe). The first day was there even before the Earth was formed. The very, very first thing that came into existance in the universe was light (scientists say that if you have a telescope powerful enough, and look far enough, you can see a huge wall of light).

God let all of his creatures (save for angels for the most part) have free will, so a creature can choose to start eating plants, or other animals or whatnot, and over time, the creature changes its’ appearance to fit their environment. When it came to man-like creatures, the way I always looked at it (and I think the pope recently mentioned something to that effect - I read it in an article somewhere) was that the first man was when God gave man a soul, and extra spark that created the first real man.

As for dinosaurs, etc., here’s a summary of what I read on the EWTN’s Q&A site - when God created all of the creatures of the Earth (Day 5 I think?), dinosaurs were included, as well as all other creatures that ever lived.

One thing to remember is that, we operate with a sense of time. We only live in 1 dimension of time (think of a timeline). We only know of now, and know what happened in the past, but can’t see the future. God is outside of time (what would that be? 4 dimensions of time? ), so time is irrelevant, since it has already happened from that viewpoint.

Interesting - I have some thinking that time radiates in all directions much like a drop of milk hitting a table. Creation was like that drop somehow.