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Author Topic:   Genuine Puzzles In Biology?
herebedragons
Member
Posts: 1498
From: Michigan
Joined: 11-22-2009


Message 46 of 153 (585451)
10-08-2010 11:38 AM
Reply to: Message 30 by Dr Jack
06-08-2010 4:36 AM


Re: Why plants are green
Although I can't come close to really answering why plants haven't evolved the ability absorb more of the visible spectrum, I believe the answer is basically that it's not about the light that is absorbed, but the pigment itself. What I mean is that chlorophyll a is very good at releasing an electron when subject to light energy. And that molecule just happens to reflect green light, it's the nature of the pigment.

But, indeed plants do have accessory pigments that allow them to absorb more of the spectrum than chlorophyll a can alone - chlorophyll b (chlorophyll c in brown algae) and carotenes. I'm not sure of the exact number, but they increase the absorption spectrum something like 100nm. However, they don’t play much of a role in actual photosynthesis, but pass on the light energy to chlorophyll a, which releases its electron to the rest of the photosynthesis process.

So, in short, chlorophyll a does the job well and the molecule appears green to our eyes. Could there be a molecule that could do it better and was a different color??? Maybe…

Now your comment about the short comings of RuBisCO presents a much more complicated puzzle. This “flaw” would be especially difficult in the early development before “modern” photosynthesis efficiency developed.

Another curious thing about photosynthesis is that oxygen is a byproduct which is actually toxic to the photosynthesis environment. This is the main role of the carotenes – to combat the free radicals. So … which would have developed first? Or why develop a process that was toxic in the first place?

Anyway, I know this doesn't solve the mystery, but actually raises more questions. Isn't science great!


This message is a reply to:
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Stephen Push
Member (Idle past 2970 days)
Posts: 140
From: Virginia, USA
Joined: 10-08-2010


Message 47 of 153 (585643)
10-08-2010 11:43 PM
Reply to: Message 1 by Dr Adequate
05-27-2010 12:05 PM


More Genuine Puzzles
Several issues in evolutionary biology have remained controversial for decades:

1) Why do most organisms grow old and die, while some (e.g., hydra) are immortal?

2) Why do so many organisms engage in sexual reproduction when asexual reproduction has the advantage of passing on ALL of one's genes to the next generation?

3) Is the individual the only important unit of selection, or does group selection play an important role in evolution?


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crashfrog
Inactive Member


Message 48 of 153 (585648)
10-09-2010 12:50 AM
Reply to: Message 47 by Stephen Push
10-08-2010 11:43 PM


Re: More Genuine Puzzles
Why do so many organisms engage in sexual reproduction when asexual reproduction has the advantage of passing on ALL of one's genes to the next generation?

Because asexual reproduction has the disadvantage of only passing on one's genes to the next generation.


This message is a reply to:
 Message 47 by Stephen Push, posted 10-08-2010 11:43 PM Stephen Push has responded

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Stephen Push
Member (Idle past 2970 days)
Posts: 140
From: Virginia, USA
Joined: 10-08-2010


Message 49 of 153 (585669)
10-09-2010 5:16 AM
Reply to: Message 48 by crashfrog
10-09-2010 12:50 AM


Re: More Genuine Puzzles
Because asexual reproduction has the disadvantage of only passing on one's genes to the next generation.

Has the Amazon molly, a unisexual fish, found a way around this problem? See

http://www.biomedcentral.com/1471-2148/8/88

Perhaps we can learn something from this little fish. Because according to the article below, high mutation rates in asexually reproducing human mitochrondria could lead to our species' extinction.

http://archive.evolution.ws/...e-l/Loewe2006-MitoRatchet.pdf

Or perhaps our mitochrondria have already evolved a solution to the disadvantage of asexual reproduction.

Edited by Stephen Push, : Correct typo.

Edited by Stephen Push, : Replaced reference to abstract with reference to full article.


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Dr Adequate
Member
Posts: 16094
Joined: 07-20-2006
Member Rating: 9.0


Message 50 of 153 (585858)
10-10-2010 5:25 AM
Reply to: Message 49 by Stephen Push
10-09-2010 5:16 AM


Re: More Genuine Puzzles
I remain to be convinced that the puzzle exists, or that any such mechanism is required.

The models which suggest that there might be a puzzle rely on the premise that there is a practically infinite supply of deleterious mutations so tiny in their effect that even in largish populations they can be fixed by drift.

Now, in our present state of understanding, if natural selection can't detect them, then nor can we: we can't just look at a genome and say: "Ah, yes, changing T to A here will incur a teensy-weensy disadvantage".

(We may also note that since mutations are discrete there must for each species be a lower bound on how little harm a mutation can do without doing no harm at all.)

So do these mutations even exist? No-one, to my knowledge, has actually shown this, or is in any position to do so. If they exist at all, there is the further question of how many of them there potentially are, which again has not been answered.

Now if hypothesizing the existence of entities the existence of which has not been demonstrated leads us to a conclusion in conflict with reality, then the most obvious conclusion is simply that this hypothesis is false, not that there is an equally undetected mechanism which counteracts the first set of undetectable entities.


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 Message 51 by Stephen Push, posted 10-10-2010 3:30 PM Dr Adequate has responded

Stephen Push
Member (Idle past 2970 days)
Posts: 140
From: Virginia, USA
Joined: 10-08-2010


Message 51 of 153 (585927)
10-10-2010 3:30 PM
Reply to: Message 50 by Dr Adequate
10-10-2010 5:25 AM


Re: More Genuine Puzzles
So do these mutations even exist? No-one, to my knowledge, has actually shown this, or is in any position to do so. If they exist at all, there is the further question of how many of them there potentially are, which again has not been answered.

You do not believe that the accumulation of deleterious mutations is a disadvantage of asexual reproduction? What do you see as the advantages of sexual reproduction (other than the fact that it's fun :-) )?

Edited by Stephen Push, : Rephrased second question.

Edited by Stephen Push, : Added smiley.


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 Message 50 by Dr Adequate, posted 10-10-2010 5:25 AM Dr Adequate has responded

Replies to this message:
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Dr Adequate
Member
Posts: 16094
Joined: 07-20-2006
Member Rating: 9.0


Message 52 of 153 (585931)
10-10-2010 3:56 PM
Reply to: Message 51 by Stephen Push
10-10-2010 3:30 PM


Re: More Genuine Puzzles
You do not believe that the accumulation of deleterious mutations is a disadvantage of asexual reproduction?

I didn't say that. But genetic meltdown models rely on a large supply of deleterious mutations too small to be detected.

(They have other problems too. For example, saving computer time by using an "infinite alleles" model that rules out the possibility of back mutations; and assuming hard rather than soft selection, both features of the paper on human mitochondria.)

I don't deny the possibility of fixation of deleterious alleles, but I have questions about how the concept is being applied.

Then what accounts for the evolution of sexual reproduction?

Apart from Muller's Ratchet? The Red Queen's Race.

(Sometimes biological nomenclature is rather fun, isn't it?)

---

I did some computer simulations of my own recently. Here's a typical result:

(In real life we would suppose that fitness has an upper limit (and that the typical organism is nearly there) and that a sufficient decrease in fitness would lead to extinction.)

Now, however one fiddles with the basic parameters, so long as beneficial mutations can happen at all it seems that there is a population size above which deleterious mutations will not manage to drive down fitness. If the real-life parameters are such that the critical population size is a quintillion, then there's a problem.

Until someone is in a position to determine the parameters, the fact that not every species is extinct suggests that this is not the case.

Edited by Dr Adequate, : No reason given.

Edited by Dr Adequate, : No reason given.


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herebedragons
Member
Posts: 1498
From: Michigan
Joined: 11-22-2009


Message 53 of 153 (586472)
10-13-2010 1:05 PM
Reply to: Message 3 by Dr Jack
05-27-2010 2:59 PM


What, exactly, is the evolutionary relationship of viruses to the rest of life and to each other?

What would make sense is this progression:

non-life (amino acids, RNA) --> "semi" life* (viruses) --> life (bacteria)

*I refered to viruses as "semi' life because they are not really considered living organisms but they do exibit some "life-like" characteristics - kind of an intermediatary.

Any evidence for this line of progression?


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herebedragons
Member
Posts: 1498
From: Michigan
Joined: 11-22-2009


Message 54 of 153 (586474)
10-13-2010 1:14 PM
Reply to: Message 1 by Dr Adequate
05-27-2010 12:05 PM


A couple things I thought of

Why do humans have such difficulty in childbirth while the rest of the animal kingdom, not so much. I have seen a calf born, and the mother basically was breathing hard for a little while then the head and shoulders came out, she stood up and the calf just fell out. No big deal. But I was with my wife when she gave birth and I thought she was being ripped in two.

Why do we have imagination? Einstein said

quote:
Imagination is more important than knowledge. For knowledge is limited to all we now know and understand, while imagination embraces the entire world, and all there ever will be to know and understand.
It is one of the characteristics that set us apart from animals. We barely understand how knowledge is stored in the brain ... can we explain imagination?
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Coyote
Member (Idle past 217 days)
Posts: 6117
Joined: 01-12-2008


Message 55 of 153 (586479)
10-13-2010 1:33 PM
Reply to: Message 54 by herebedragons
10-13-2010 1:14 PM


Extended infancy
Why do humans have such difficulty in childbirth while the rest of the animal kingdom, not so much.

That has to do with the large brains humans have.

Babies come out totally helpless and remain that way for several years, and its still a very tight squeeze.

That's the trade-off for the large brains: the extended infancy permitted by our culture allows helpless infants to survive.

Prey animals have to be up and on their feet within a very short time. Young horses can get around pretty well within hours.


Religious belief does not constitute scientific evidence, nor does it convey scientific knowledge.
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Dr Adequate
Member
Posts: 16094
Joined: 07-20-2006
Member Rating: 9.0


Message 56 of 153 (586480)
10-13-2010 1:40 PM
Reply to: Message 54 by herebedragons
10-13-2010 1:14 PM


Why do humans have such difficulty in childbirth while the rest of the animal kingdom, not so much.

We have relatively big heads, and our pelvises are adapted to walking upright.

Why do we have imagination?

Well, it's useful. In order to be able to plan ahead, we have to be able to say to ourselves: "What would happen if I do such-and-such a thing?"

It is one of the characteristics that set us apart from animals.

This is not clear. For example, the following has been observed. A chimp is set a puzzle where the reward is bananas. She tries to solve it, and fails. She sits staring at it for a few minutes. Then she gives a great whoop, turns a backflip ... and then solves the puzzle and acquires the bananas.

The point is, she knew that she had solved the puzzle before she actually got the bananas, because she was capable of thinking: if I do this, then bananas will ensue.


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Nuggin
Member (Idle past 603 days)
Posts: 2965
From: Los Angeles, CA USA
Joined: 08-09-2005


Message 57 of 153 (586500)
10-13-2010 3:20 PM
Reply to: Message 54 by herebedragons
10-13-2010 1:14 PM


Imagination

(Imagination) is one of the characteristics that set us apart from animals. We barely understand how knowledge is stored in the brain ... can we explain imagination?

Anyone who has ever spent more than a few minutes with a cat knows that humans are not the only creatures with imagination.

I had a cat years ago that would spontaneously attack an otherwise empty spot on the wall, then bolt from the room as if its tail was on fire.

I have no doubt that our language skills and knack for abstract thought gives us a different sort of imagination than is experienced by various animals - however, I can't fathom a means by which this claim could be tested definitively.


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Stephen Push
Member (Idle past 2970 days)
Posts: 140
From: Virginia, USA
Joined: 10-08-2010


Message 58 of 153 (586504)
10-13-2010 3:53 PM
Reply to: Message 56 by Dr Adequate
10-13-2010 1:40 PM


Free Will
Well, it's useful. In order to be able to plan ahead, we have to be able to say to ourselves: "What would happen if I do such-and-such a thing?"

Intuitively I agree with this account of the value of imagination. But as a scientific explanation it seems problematic because it presupposes the existence of free will, a property that appears to defy scientific analysis. Is there any way to establish that free will actually exists, not to mention how it could have evolved?

Edited by Stephen Push, : Corrected typo.


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Dr Adequate
Member
Posts: 16094
Joined: 07-20-2006
Member Rating: 9.0


Message 59 of 153 (586517)
10-13-2010 5:00 PM
Reply to: Message 58 by Stephen Push
10-13-2010 3:53 PM


Re: Free Will
Intuitively I agree with this account of the value of imagination. But as a scientific explanation it seems problematic because it presupposes the existence of free will ...

It does? Where?

I do in fact believe in free will, but I don't see that my explanation of the practical value of the imagination contains anything that would perturb the strictest incompatibilist determinist.


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Stephen Push
Member (Idle past 2970 days)
Posts: 140
From: Virginia, USA
Joined: 10-08-2010


Message 60 of 153 (586525)
10-13-2010 5:38 PM
Reply to: Message 59 by Dr Adequate
10-13-2010 5:00 PM


Re: Free Will
Well, it's useful. In order to be able to plan ahead, we have to be able to say to ourselves: "What would happen if I do such-and-such a thing?"

By way of suggesting a practical value of imagination, you seem to be describing a conversation with yourself in which you choose from two or more options. That seems to suggest the exercise of free will. Unless this internal conversation is just an illusion without effect on the outcome. But if so, where is the practical value?
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