What are the Weaknesses of Evolution?

[Split Rock]

That would mean that malaria is caused by a plant. I think my colleagues who study malaria would be surprised to learn that they were now botanists.

Interesting. I didn't know that Plasmodium species have a plastid. We could say that organisms with chloroplasts are plants, but that would leave out parasitic plants like Dodder.

I know, all plant species are plants! There that should settle it...

 

[Wiccan_Child]

I know, all plant species are plants! There that should settle it...

But what if they're not?

 

[sfs]

Interesting. I didn't know that Plasmodium species have a plastid.

Apparently at some point an ancestor of Plasmodium ingested a plant and decided it liked the chloroplast and kept it -- the second time the chloroplast became a symbiont. By this time its no longer photosynthetic, and has been reduced to the apicoplast. What exactly it does for the parasite is unclear.

 

[BigDug]

If your chart is based on the Kimura paper you cited, then your description of it is wrong. Kiimura's paper does not describe the real distribution of mutation effects in the human population
...
In other words, he simply assumed the shape of the distribution.

Well the Kimura study is theoretical, yet the curve shape is accurate,so I am not so sure I agree with you. The reason is:

His curve is wrong, and massively so, for human mutations. First, note that ~95% of the genome seems to have no function, so that fraction of mutation will be completely neutral. Of the remaining mutations, a much larger fraction than the curve would suggest are highly deleterious, enough so to be removed by natural selection.

Consider just the coding regions of genes, which are the parts of the genome that are the best understood. They are about 1.5% of the genome, or 50 million base pairs. Single base subsitutions (easily the most common mutations) within coding regions either change the amino acid that is coded for (nonsynonymous) or don't (synonymous). Roughly two-thirds of substitutions are nonsynonymous. Of these, approximately 75% are deleterious enough to be removed by selection. (This can be seen both in within-species studies (Nature Genetics 22:231 (1999)) and in comparing humans and chimpanzees (Nature 437:69 (2005).) That means that fully half of all mutations are to the left of Kimura's box, which isn't at all consistent with his curve.

I think the mutations being shown here include the whole genome, including the aforementioned ~95% which you had stated as "completely neutral". I think thats why the larger frequency of total mutations are counted, the closer they pile up towards 0. I am curious as to why you don't think the entire genome would not be included in the graph.

OK. Well lets move on...

Of the remaining mutations, some undoubtedly are mildly deleterious, and accumulate freely in the genomes of organisms like humans. For many of them, the selective disadvantage is tiny, and the correct response is, "So what?". Being slightly less fit relative to a perfect member of your species isn't very important to evolution, when the perfect member doesn't exist; you only compete against real organisms, not ideal ones.

There is an intermediate range of mildly deleterious mutations that are more interesting, however. These have a selective disadvantage too small to be eliminated by selection in the human population, but large enough that the effects become significant as more and more mutations pile up. For example, synonymous mutations don't change the protein, but for highly expressed genes they may slow production of the protein down by a bit, since the translation machinary is forced to use less common transfer RNAs. So if you start with optimal production, repeated synonymous mutations may gradually make the expression level of the protein lower and lower, leading to a less (healthy, happy, bouncy, whatever) organism.

Does this spell disaster (i.e. extinction) for the species? Well, no. As the species drifts towards lower and lower fitness as a result of changes at that gene, the opportunity for beneficial mutations increases; the farther you are from perfect fitness, the more likely it is that a change will be good for you. In this case, a mutation that increases transcription of the gene will have a substantial benefit, and will be favored by natural selection.

Ok. Well the question becomes: How much mutation is too much? This is where evolution begins to become a tautology, especially when there seems to be a mindset which places no limit to the rescuing power of natural selection.

Human mutation rates are much too high. For decades geneticists have been worried about the impact of mutations on the human population.(Muller 1950, Crow 1997)
Muller, American Journal Human Genetics 2:111-176
http://www.pnas.org/cgi/content/full/94/16/8380

When these concerns first arose, they were based on a rate of deleterious mutation of .12 to .30 per person per generation(Muller 1956)
http://www.pnas.org/cgi/reprint/42/11/855

Also there was a concern that if the rate got as high as 1 per person per generation, then their would be a real problem with long-term deterioration.

That would be a real problem because there would be no way to get rid of the deleterious mutations, we would need to keep the number below .33 per person per generation in order to select out the bad mutation and have two people left to reproduce and continue a healthy population.

So needless to say, good geneticists are not just saying "so what?" about mutation rates, rather they would tend to watch mutation rates very closely.

So back to our original numbers and questions: even if we accept estimates of Kondrashov, Nachman and Crowell about the amount of mutation to be ~200, which we had tentatively agreed on, and we consider 95% of the genome to be as you said: "completely neutral" (or junk), what is the new bottom line? 95% of 200 = 190 leaving 10 deleterious mutations per person.

So I would be eager to find out what kind of selection structure is going to halt this kind of deterioration.

*Also bearing in mind that this number 200 is a low, conservative estimate.

**Also the portion of the genome that is recognized as truly functional is quickly rising from 95%.

***These are just the point mutations, not counted are the other types:deletions,insertions,duplications,translocations,inversions, and mitochondrial mutations.

I don't know what you mean, but it sounds wrong. Natural selection operates at the level of the organism.

Whoops. Reverse that, my dislexia was kicking in, I meant the opposite. Sorry.

You are misunderstanding something fundamental here. The rate of beneficial mutations depends strongly on the environment (something Kimura actually points out in this paper). It has to. The beneficial mutation rate for an organism that is perfectly adapted to its current environment must be zero, since "perfectly adapted" means it can't get any better. Change the environment, and suddenly there are ways the organism could be improved, and so the beneficial mutation rate will go up.

There was a paper within the last few weeks in Science that reported a very nice series of experiments with bacteria (E. coli), measuring the beneficial mutation rate in an environment where the bacterium was not well adapted. They measured a beneficial mutation rate of the greater than 1 per 100,000 bacteria (i.e. 10^-5/genome replication). The total mutation rate for E. coli is only about 1 mutation per 400 replications, so the beneficial mutation rate in this environment was on the order of 1% of all mutations, which is enormous.

OK obviously your very knowledgeable about the subject, and you actually have years of experience and lots more knowledge than me, so let me ask you a question,...based upon the above quote:

You have shown this high frequency of E.Coli mutation, tested against a background which they were not adapted to,...why do we not see some major evolutionary progress with these types of experiments?

If we have figured out ways to engineer high mutation rates in bacteria, and their reproduction levels are so high combined with short lifespans we are able to see thousands of such generations...correct?

Why wont they evolve into eukaryotes? And if they wont, then why did we?(allegedly) I assume the answer is that the procaryote->eukaryote jump was just such a big one.

Regardless of your answer, I would think that the E.coli would make an excellent testable subject for the ToE.

Or maybe corn, or bigger roses. I dont know, Im getting tired.

 

[BigDug]

Nothing went bang, per se. The term was coined by it's opponents.
The 'Big Bang' was the rapid expansion of the spacetime continuum from a timeless, spaceless singularity.

Yeah, I think what Inan3 is asking is the fundamental question of the origins of all matter. In other words,...where did it all come from? And if I understand correctly, there is no generally accepted theories for the exact origins of all matter. Just like there are no generally accepted theories of abiogenesis. There are lots of explanations out there, but there is no generally accepted theories that I'm aware of. However in the end it really doesnt matter what is 'generally accepted' and what is not, the truth is the only thing that matters.

 

[ngpty]

Ok. Next I'll show that mutations can indeed cause a "loss of information" and that it is not just a creationist wording, but that it also exists in many science books and publications as well. But more importantly I'll discuss the relevance of it.

Trivial to do. However, showing that mutation can cause a loss of information would suprise no-one -- if you want to demonstrate that mutation cannot cause speciation you must demonstrate that mutation must not ever cause an increase in information. Good luck with that.

Of course I'll also build upon more of this genetic entropy hypothesis also, while at the same time trying to at least read, but definitely get to any feedback I might get.

What kind of entropy? If you are talking about thermodynamic entropy, then you are looking at the wrong place -- life is all about exploiting waste energy and (therefore) increasing entropy, but that has nothing to do with how complex a life form is or its particular evolutionary history. If you are talking about Shannon entropy, then every mutation increases entropy, but that is because Shannon information theory is solely concerned with what it takes to perfectly copy a given message -- it does not care about what the message says or how to interpret the message. The only measure of entropy that seems to apply is entropy defined in terms of Chaitin information theory, and since Chaitin information theory uses several key concepts from computer science (Turing machines, compressibility, etc.), you will have a fun time determining what specific mutations even mean in terms of entropy.

(also, if you manage to do that, computational biologists will beat a path to your door).

 

[MarcusHill]

Because that is what we are like, (minus the omnipotence). We are creative. We decide. We have life. We love. We appreciate. We have reasoning. We increase. We are more than energy. We have soul and spirit. Like God. We are like our Creator.

So it's easier to believe in a self-existing being than self-existing energy because the self-existing being is like us. That's odd. We're pretty complicated, adding omnipotence would make us more so, a bunch of energy is pretty simple. I'd tend to think something simple is more likely to "just exist" than something complex.

I think you're putting the cart in front of the horse. God didn't create us in his image, we created him in ours. In fact, your statement that it's easier for you to believe in a self-existent being "because that is what we are like" would tend to give credence to this claim.

 

[Inan3]

So it's easier to believe in a self-existing being than self-existing energy because the self-existing being is like us. That's odd. We're pretty complicated, adding omnipotence would make us more so, a bunch of energy is pretty simple. I'd tend to think something simple is more likely to "just exist" than something complex.

I think you're putting the cart in front of the horse. God didn't create us in his image, we created him in ours. In fact, your statement that it's easier for you to believe in a self-existent being "because that is what we are like" would tend to give credence to this claim.

Well, I can agree with you that we are complicated and complex.

That is not the only reason that I believe in a God that existed before all and created all but it does seem more reasonable to me that a complex intelligent being had more to do with all that I know and see than an energy form.

I'm not sure but it seems that evolution goes from the simple to complex argument and if I'm right in this, I can see how you would think that we came from self existing energy.

I do know that it is each persons perogative to believe as they want. I just choose it to be by design rather than happenstance.

 

[MarcusHill]

I'm not sure but it seems that evolution goes from the simple to complex argument and if I'm right in this, I can see how you would think that we came from self existing energy.

Just to be clear on a couple of points:

Firstly, evolution has nothing to do with the origins of the universe. The Big Bang theory and other aspects of cosmology explain how we went from simple energy and elements to the range of elements arrayed in stars, planets and so forth in the universe.

Secondly, I don't think we came from self-existing energy, merely that this hypothesis is more feasible than a self-existing intelligent being. The jury is still very much out on the pre-Planck universe, and my best answer as to what I actually believe was the origin of that singularity and what caused it to expand is "we don't know yet".

 

[Inan3]

However in the end it really doesnt matter what is 'generally accepted' and what is not, the truth is the only thing that matters.

Agreed and I'll go even further to say that Truth, being the Word of God and spiritual is greater than fact. Truth can actually change fact.

Jhn 17:17 Sanctify them through thy truth: thy word is truth.

2Cr 4:18 While we look not at the things which are seen, but at the things which are not seen: for the things which are seen [are] temporal; but the things which are not seen [are] eternal.

Jhn 6:63 It is the spirit that quickeneth; the flesh profiteth nothing: the words that I speak unto you, [they] are spirit, and [they] are life.

Mar 11:13-14 & 20 And seeing a fig tree afar off having leaves, he came, if haply he might find any thing thereon: and when he came to it, he found nothing but leaves; for the time of figs was not [yet]. And Jesus answered and said unto it, No man eat fruit of thee hereafter for ever. And his disciples heard [it]....And in the morning, as they passed by, they saw the fig tree dried up from the roots.

Gen 1:3 And God said....
Gen 1:6 And God said....
Gen 1:9 And God said....
Gen 1:11 And God said....
Gen 1:14 And God said....
Gen 1:20 And God said....
Gen 1:24 And God said....
Gen 1:26 And God said....

Psa 33:6 By the word of the LORD were the heavens made; and all the host of them by the breath of his mouth.

Hbr 11:3 Through faith we understand that the worlds were framed by the word of God, so that things which are seen were not made of things which do appear.

2Pe 3:5 For this they willingly are ignorant of, that by the word of God the heavens were of old, and the earth standing out of the water and in the water:

 

[Edx]

Agreed and I'll go even further to say that Truth, being the Word of God and spiritual is greater than fact. Truth can actually change fact.

Huh? How can truth be different to fact?

 

[Wiccan_Child]

Yeah, I think what Inan3 is asking is the fundamental question of the origins of all matter.

And I gave it: ~13 billion years ago, there was no matter, no energy, no spacetime. Then* there was: the singularity began to expand, and matter/energy formed.

*Insofar as we our time-based language applies to a timeless scenario.

In other words,...where did it all come from? And if I understand correctly, there is no generally accepted theories for the exact origins of all matter.

Like I said, the Big Bang.

Just like there are no generally accepted theories of abiogenesis. There are lots of explanations out there, but there is no generally accepted theories that I'm aware of.

The most widely accepted theory of abiogenesis is the 'primordial soup' model supported by the Miller-Urey experiments.

However in the end it really doesnt matter what is 'generally accepted' and what is not, the truth is the only thing that matters.

Indeed. And the scientific consensus falls on whatever explanation is most likely to be true.

 

[Inan3]

Indeed. And the scientific consensus falls on whatever explanation is most likely to be true.

Pretty shaky ground if you ask me.

 

[Inan3]

And I gave it: ~13 billion years ago, there was no matter, no energy, no spacetime. Then* there was: the singularity began to expand, and matter/energy formed.

So this must be the "scientific consensus which falls on whatever explanation is most likely to be true" for this day and hour?

And this is the voice of reason? I don't get it, except that the scriptures says that men "willingly" choose to be ignorant of God and His creation. Well, it is a choice. Not mine but it is a choice.

2Pe 3:5 For this they willingly are ignorant of, that by the word of God the heavens were of old, and the earth standing out of the water and in the water:

 

[Inan3]

Huh? How can truth be different to fact?

Truth comes from God which will never change whereas fact is only fact until a better conclusion is made.

 

[Edx]

Truth comes from God which will never change whereas fact is only fact until a better conclusion is made.

How do you know the truth is "from god". You only have faith that your scriptures are. They are still written by men, you believe they are something more.

Secondly, if a fact wasnt true then it wasnt really a fact to begin with.

 

[Inan3]

Why does it seem that you guys are coming out of the woodwork? First we have one group of posters and then another and when you can't handle those who have a little more info (not me) you call in those from MIT. Do you all go online or to the phones and enlist your buddies and mentors? No problem but seems suspect to me.

 

[Inan3]

How do you know the truth is "from god". You only have faith that your scriptures are. They are still written by men, you believe they are something more.

Secondly, if a fact wasnt true then it wasnt really a fact to begin with.

How do I know? I know the One Who gives truth.

Being true and being truth are different.

 

[Tomk80]

Why does it seem that you guys are coming out of the woodwork? First we have one group of posters and then another and when you can't handle those who have a little more info (not me) you call in those from MIT. Do you all go online or to the phones and enlist your buddies and mentors? No problem but seems suspect to me.

My guess is that many are just reading and respond when they feel they have anything to add. At least that's what I do. Especially since I'm pretty busy this week and can't really address anything in depth.

 

[Wiccan_Child]

Pretty shaky ground if you ask me.

You say this using a computer. Maxwell's (scientific) laws govern computers.
Do you think that you would be alive were it not for modern medicine?
Do you think we could have put men on the Moon, and probed the deepest galaxies, without science?

So this must be the "scientific consensus which falls on whatever explanation is most likely to be true" for this day and hour?

Unless a more probable explanation has been devised, yes.

And this is the voice of reason?

Yes. I'm not entirely sure what you're getting at, but yes.

I don't get it, except that the scriptures says that men "willingly" choose to be ignorant of God and His creation. Well, it is a choice. Not mine but it is a choice.

2Pe 3:5 For this they willingly are ignorant of, that by the word of God the heavens were of old, and the earth standing out of the water and in the water:

Since I do not believe the Bible to contain an iota of truth, you won't mind if I gloss past this offensive claim.

Why does it seem that you guys are coming out of the woodwork? First we have one group of posters and then another and when you can't handle those who have a little more info (not me) you call in those from MIT. Do you all go online or to the phones and enlist your buddies and mentors? No problem but seems suspect to me.

Have you ever heard of lurkers? They who watch the thread but do not post in it. As you make more and more outlandish statements, more and more lurkers feel compelled to reply. It is a purely natural system that only appears to be designed .