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The two-facedness of biology

Use this forum to discuss the philosophy of science. Philosophy of science deals with the assumptions, foundations, and implications of science.
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Mysterio448
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The two-facedness of biology

Post by Mysterio448 » January 2nd, 2015, 4:26 pm

There is something that I have noticed about biology that I found interesting. It seems that biology is "two-faced." What I mean by this is that it seems every function of the body possesses some flaw that is inherent to its very design. Furthermore, in many cases bodily functions that are keeping us alive are also, ironically, trying to kill us. After doing a little research, I can list a few examples of this strange phenomenon:

1) The pharynx. This is the passage in the throat used for both swallowing and breathing. The pharynx presents to us the very real danger of choking while swallowing food or drink.

2) The blind spot of the human eye. It is a result of the spot on the retina that lacks photoreceptors in order to make way for the optic nerve. Because of this absence of photoreceptors, there is a small spot in our visual field where we are essentially blind (although the brain usually will interpolate around the spot in order to mask it from our consciousness).

3) The electron transport chain. This is a complex process, occurring in cellular mitochondria, that is the body's primary producer of ATP, which is the body's main energy source. However, this process is also simultaneously responsible for releasing various free radicals into the body, such as superoxide anion, hydrogen peroxide, and hydroxyl free radical. These free radicals contribute to aging and diseases such as type 2 diabetes and Parkinson's disease.

4) DNA replication. Before cells undergo cell division, their DNA are first replicated. After the two strands of DNA are "unzipped" from each other, a protein called DNA polymerase travels along each strand using them as templates to make copy DNA strands. However, the two parent strands are not completely separated before this process; they are copied as they are being separated from each other. So while the DNA polymerase can copy one parent strand continuously, to avoid copying in the wrong direction it can only copy the other strand in fragments, and only after the fragments are preceded by a short nucleotide sequence called an RNA primer. The problem with this process is that when the DNA polymerase gets to the end of the DNA strand, there is nowhere for the RNA primer to attach to, thus the RNA polymerase cannot copy anymore DNA at this point. Technically, this should lead to gradual loss of DNA information with subsequent cell divisions. In reality, this design flaw is mitigated by redundant DNA sequences called telomeres, but this only delays DNA degradation rather than preventing it. Telomere shortening is an inevitable process that subsequently contributes to aging and death.

5) Coagulation. A vital physiological process which forms a plug (blood clot) on the walls of a blood vessel that has been damaged, thus preventing dangerous hemorrhaging. However, these same plugs also run the risk of accidentally detaching from their point of origin and becoming an "embolus" that can freely travel along the blood flow. This can likely impede blood flow and cause serious health problems or death.

6) The immune system. This vital system protects the body from pathogens and harmful irritants. However, the immune system can also itself injure the body. Inflammation, normally a helpful part of the immune system, can often lead to chronic inflammation, which can be a serious health problem. Autoimmune diseases (such as arthritis, lupus, and multiple sclerosis) are diseases in which the immune system begins attacking the body's own tissues, treating them as if they were an infectious pathogen.

7) Cellular structure. Scientists have learned that cancer is actually a natural result of the normal cellular dynamics of the body. The disease is inevitable; everyone will eventually get it, provided they live long enough. A scientific article in Wired Magazine says that there is a "misguided notion that cancer cells are fundamentally different from their normal counterparts.” According to oncology researcher Jarle Breivik, "[Cancer is] the inevitable consequence of our multicellular composition." He says that multicellular organisms are themselves evolutionary systems in which mutation and natural selection occur all the time. Furthermore he says, "The cells of your body are genetically programmed to collaborate, but as we age and new mutations appear, natural selection will favor those mutants that break away from the control mechanisms and proliferate.” So cancer is "an inescapable byproduct of multicellularity and long lifespans." Ironically, the same multicellular structure that constitutes the body is also slowly tearing the body down.

So what do you make of this? Do you agree with my observation that biology is inherently two-faced? And if so, why do you think this is?

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Re: The two-facedness of biology

Post by Obvious Leo » January 3rd, 2015, 12:01 am

Mysterio448 wrote: Do you agree with my observation that biology is inherently two-faced? And if so, why do you think this is?
I agree completely. Your examples are beautifully illustrative and I could add dozens more such as the torturous path around vital organs taken by the vagus nerve and the utterly ridiculous ball joint which passes for a human hip.

I used to think the intelligent designer must have shown up drunk to work the day he was doing homo sapiens but as it turns out all species have similar issues. It's just the way evolution works. Evolution is the epitome of ad hoc, "near enough is good enough" compromise. As far as nature is concerned we only need to live long enough to reproduce and what happens to us after that is none of her concern. What about the peacock's tail? Its big and bright enough to catch the eye of a predator from a mile way. Nature couldn't care less as long as the peahen gets to see it first and is suitably impressed.

Regards Leo

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Re: The two-facedness of biology

Post by Misty » January 3rd, 2015, 5:53 am

Mysterio448 wrote:There is something that I have noticed about biology that I found interesting. It seems that biology is "two-faced." What I mean by this is that it seems every function of the body possesses some flaw that is inherent to its very design. Furthermore, in many cases bodily functions that are keeping us alive are also, ironically, trying to kill us. After doing a little research, I can list a few examples of this strange phenomenon:

1) The pharynx. This is the passage in the throat used for both swallowing and breathing. The pharynx presents to us the very real danger of choking while swallowing food or drink.

2) The blind spot of the human eye. It is a result of the spot on the retina that lacks photoreceptors in order to make way for the optic nerve. Because of this absence of photoreceptors, there is a small spot in our visual field where we are essentially blind (although the brain usually will interpolate around the spot in order to mask it from our consciousness).

3) The electron transport chain. This is a complex process, occurring in cellular mitochondria, that is the body's primary producer of ATP, which is the body's main energy source. However, this process is also simultaneously responsible for releasing various free radicals into the body, such as superoxide anion, hydrogen peroxide, and hydroxyl free radical. These free radicals contribute to aging and diseases such as type 2 diabetes and Parkinson's disease.

4) DNA replication. Before cells undergo cell division, their DNA are first replicated. After the two strands of DNA are "unzipped" from each other, a protein called DNA polymerase travels along each strand using them as templates to make copy DNA strands. However, the two parent strands are not completely separated before this process; they are copied as they are being separated from each other. So while the DNA polymerase can copy one parent strand continuously, to avoid copying in the wrong direction it can only copy the other strand in fragments, and only after the fragments are preceded by a short nucleotide sequence called an RNA primer. The problem with this process is that when the DNA polymerase gets to the end of the DNA strand, there is nowhere for the RNA primer to attach to, thus the RNA polymerase cannot copy anymore DNA at this point. Technically, this should lead to gradual loss of DNA information with subsequent cell divisions. In reality, this design flaw is mitigated by redundant DNA sequences called telomeres, but this only delays DNA degradation rather than preventing it. Telomere shortening is an inevitable process that subsequently contributes to aging and death.

5) Coagulation. A vital physiological process which forms a plug (blood clot) on the walls of a blood vessel that has been damaged, thus preventing dangerous hemorrhaging. However, these same plugs also run the risk of accidentally detaching from their point of origin and becoming an "embolus" that can freely travel along the blood flow. This can likely impede blood flow and cause serious health problems or death.

6) The immune system. This vital system protects the body from pathogens and harmful irritants. However, the immune system can also itself injure the body. Inflammation, normally a helpful part of the immune system, can often lead to chronic inflammation, which can be a serious health problem. Autoimmune diseases (such as arthritis, lupus, and multiple sclerosis) are diseases in which the immune system begins attacking the body's own tissues, treating them as if they were an infectious pathogen.

7) Cellular structure. Scientists have learned that cancer is actually a natural result of the normal cellular dynamics of the body. The disease is inevitable; everyone will eventually get it, provided they live long enough. A scientific article in Wired Magazine says that there is a "misguided notion that cancer cells are fundamentally different from their normal counterparts.” According to oncology researcher Jarle Breivik, "[Cancer is] the inevitable consequence of our multicellular composition." He says that multicellular organisms are themselves evolutionary systems in which mutation and natural selection occur all the time. Furthermore he says, "The cells of your body are genetically programmed to collaborate, but as we age and new mutations appear, natural selection will favor those mutants that break away from the control mechanisms and proliferate.” So cancer is "an inescapable byproduct of multicellularity and long lifespans." Ironically, the same multicellular structure that constitutes the body is also slowly tearing the body down.

So what do you make of this? Do you agree with my observation that biology is inherently two-faced? And if so, why do you think this is?
I would not say two faced but I would say creation is a marvelous feat by an incredible intelligence. Life and death created to coexist making life death and death life. There are no flaws in creation, just humans who don't appreciate the conundrum and judge from limited knowledge.
Things are not always as they appear; it's a matter of perception.

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Re: The two-facedness of biology

Post by Atreyu » January 3rd, 2015, 12:22 pm

Yes, this is an interesting observation, Mysterio. I like to express it like this: life and death go hand in hand, you cannot have the one without the other. This means that we are dying from the moment of conception. Therefore, our existence on earth is really a duality, the result of the interaction of two opposing forces. And this, to me, suggests that life, or rather, life/death (our existence) is actually a cyclical (recurring) phenomena, rather than a linear (non-recurring) phenomena, as many people seem to believe.

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Re: The two-facedness of biology

Post by Theophane » January 3rd, 2015, 1:52 pm

Do you agree with my observation that biology is inherently two-faced?

As human beings, we're definitely cheated out of health, youth, and wholeness during the course of our lives. Medical science can perform wonders to provide us with longer & healthier lives, yet the logos of our bodies bears the indelible stamp of what you call "two-facedness." You've seen photos of ageing celebrities who've undergone many cosmetic surgical procedures to maintain their youthful appearance? It doesn't work, does it? Our biological frailty is inescapable.


(Nested quote removed.)
I think it's how nature works. The impermanence, the frailty.

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Re: The two-facedness of biology

Post by Mysterio448 » January 4th, 2015, 10:30 am

Obvious Leo wrote:
Mysterio448 wrote: Do you agree with my observation that biology is inherently two-faced? And if so, why do you think this is?
I agree completely. Your examples are beautifully illustrative and I could add dozens more such as the torturous path around vital organs taken by the vagus nerve and the utterly ridiculous ball joint which passes for a human hip.

I used to think the intelligent designer must have shown up drunk to work the day he was doing homo sapiens but as it turns out all species have similar issues. It's just the way evolution works. Evolution is the epitome of ad hoc, "near enough is good enough" compromise. As far as nature is concerned we only need to live long enough to reproduce and what happens to us after that is none of her concern. What about the peacock's tail? Its big and bright enough to catch the eye of a predator from a mile way. Nature couldn't care less as long as the peahen gets to see it first and is suitably impressed.

Regards Leo
But isn't it strange that most of these biological mistakes aren't just design flaws (such as the blind spot), but are actively antagonistic to our survival? It's as if we have been sabotaged by our own bodies. I can understand that, because of how evolution works, our bodies are not perfect, but why must they be sabotaged?

Theophane wrote:
Do you agree with my observation that biology is inherently two-faced? (Nested quote removed.)
I think it's how nature works. The impermanence, the frailty.
Why do you think nature works this way?

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Re: The two-facedness of biology

Post by Theophane » January 4th, 2015, 1:27 pm

“The total amount of suffering per year in the natural world is beyond all decent contemplation. During the minute that it takes me to compose this sentence, thousands of animals are being eaten alive, many others are running for their lives, whimpering with fear, others are slowly being devoured from within by rasping parasites, thousands of all kinds are dying of starvation, thirst, and disease. It must be so. If there ever is a time of plenty, this very fact will automatically lead to an increase in the population until the natural state of starvation and misery is restored. In a universe of electrons and selfish genes, blind physical forces and genetic replication, some people are going to get hurt, other people are going to get lucky, and you won't find any rhyme or reason in it, nor any justice. The universe that we observe has precisely the properties we should expect if there is, at bottom, no design, no purpose, no evil, no good, nothing but pitiless indifference.”


― Richard Dawkins, River Out of Eden: A Darwinian View of Life
There you have it. Pitiless indifference.

This is not a worldview I personally share, of course, but godless people tend to stop asking these questions once they get an answer that brutally extinguishes love, hope, and joy. Abandon All Hope, Ye Who Enter Through Here.

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Re: The two-facedness of biology

Post by David_the_simple » January 4th, 2015, 1:44 pm

Mysterio448 wrote:There is something that I have noticed about biology that I found interesting. It seems that biology is "two-faced." What I mean by this is that it seems every function of the body possesses some flaw that is inherent to its very design. Furthermore, in many cases bodily functions that are keeping us alive are also, ironically, trying to kill us. After doing a little research, I can list a few examples of this strange phenomenon: ...

So what do you make of this? Do you agree with my observation that biology is inherently two-faced? And if so, why do you think this is?
I can see your perspective, but allow me to share mine.

These points you brought out are designs that work, it allows the entity to perform their functions.

Also as you pointed out, these designs are not fine tuned and leave room for improvement through natural mechanisms.

In another perspective, life's designs are in constant need of fine tuning.

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Re: The two-facedness of biology

Post by Obvious Leo » January 4th, 2015, 7:25 pm

Mysterio448 wrote: But isn't it strange that most of these biological mistakes aren't just design flaws (such as the blind spot), but are actively antagonistic to our survival? It's as if we have been sabotaged by our own bodies. I can understand that, because of how evolution works, our bodies are not perfect, but why must they be sabotaged?
This question is surprisingly easy to answer. If organisms didn't do the right thing and die after passing on their genetic material then the biosphere would be overpopulated in a heartbeat. Evolution is driven by death and the resources of our planet are finite. Without death these resources would be quickly depleted and then what happens to our living creatures?

You guessed it. They die anyway. Immortality is an unrealisable abstraction.

Regards Leo

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Re: The two-facedness of biology

Post by Mysterio448 » January 4th, 2015, 9:02 pm

Obvious Leo wrote:
Mysterio448 wrote: But isn't it strange that most of these biological mistakes aren't just design flaws (such as the blind spot), but are actively antagonistic to our survival? It's as if we have been sabotaged by our own bodies. I can understand that, because of how evolution works, our bodies are not perfect, but why must they be sabotaged?
This question is surprisingly easy to answer. If organisms didn't do the right thing and die after passing on their genetic material then the biosphere would be overpopulated in a heartbeat. Evolution is driven by death and the resources of our planet are finite. Without death these resources would be quickly depleted and then what happens to our living creatures?

You guessed it. They die anyway. Immortality is an unrealisable abstraction.

Regards Leo

So are you basically saying that the built-in sabotaging of the body is not an accident but is all a part of nature's plan? Like a biological fail-safe?

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Re: The two-facedness of biology

Post by Obvious Leo » January 4th, 2015, 9:57 pm

Mysterio448 wrote: So are you basically saying that the built-in sabotaging of the body is not an accident but is all a part of nature's plan? Like a biological fail-safe?
Exactly. I don't like the term "nature's plan" because of its teleological overtones but I don't think this is the sense in which you meant it. Nature has no plan. She just does what she does because she cannot do otherwise. The appearance of purpose is an effect rather than a cause. Only minds can have purpose.

Regards Leo

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Re: The two-facedness of biology

Post by Greta » January 5th, 2015, 12:25 am

“The total amount of suffering per year in the natural world is beyond all decent contemplation. During the minute that it takes me to compose this sentence, thousands of animals are being eaten alive, many others are running for their lives, whimpering with fear, others are slowly being devoured from within by rasping parasites, thousands of all kinds are dying of starvation, thirst, and disease. It must be so. If there ever is a time of plenty, this very fact will automatically lead to an increase in the population until the natural state of starvation and misery is restored. In a universe of electrons and selfish genes, blind physical forces and genetic replication, some people are going to get hurt, other people are going to get lucky, and you won't find any rhyme or reason in it, nor any justice. The universe that we observe has precisely the properties we should expect if there is, at bottom, no design, no purpose, no evil, no good, nothing but pitiless indifference.”

― Richard Dawkins, River Out of Eden: A Darwinian View of Life
Theophane wrote:There you have it. Pitiless indifference.

This is not a worldview I personally share, of course, but godless people tend to stop asking these questions once they get an answer that brutally extinguishes love, hope, and joy. Abandon All Hope, Ye Who Enter Through Here.
I agree, Theo, as would most of us. I don't share the worldview of pitiless indifference. Nor does Richard Dawkins. He has frequently stated that "nature red in tooth and claw" need not be our fate, that we can choose to be kinder.

However, the observation is a poignant one, given the incomprehensible level of suffering in the wild.

I think it likely that humanity will rise up again from the problems of the next few centuries. We will gradually develop more of the good human qualities - intelligence, wisdom, rationality, civility, honesty, decency and kindness and reduce our negative animal qualities like greed, pride, aggression, selfishness, obtuseness, cruelty and indifference. I would like to think that the process of improvement will continue for a very long time, although there will always be the occasional step or two backward along the way (always seemingly interpreted by the affected societies at the time as everything going to hell in a handbasket). Meanwhile the Earth will be transformed, and much will be destroyed in the process. Most of the suffering animals will suffer but we will miss our fellow travellers.

While we know that destruction is necessary in order for nature to rebuild and that environmental destruction is an inevitable product of our current civilisations, I think it's worthwhile to resist the destruction in whatever small way we can, be it through recycling, being careful with resource usage, donating or working.

We can accept the environmental realities but still do whatever we can to slow it rather than give in to apathy or learned helplessness. Who knows what razor thin margins of error our descendants will be dealing with in the future? Perhaps the efforts we make (or don't make) today will make the difference?

Our efforts could also be akin to spitting into a tidal wave. We don't know. The one thing we can do is preserve what we are able and hope for the best. That's more or less the difference between accepting the dynamics of nature and aiming to transcend it. Even if the large "machines" of the universe and the Earth will crush us should we be unlucky enough to be in their paths, we at least have the capability to make our small, local part of the universe more kind, but we have to overcome some evolutionary baggage to do so.

-- Updated 04 Jan 2015, 23:27 to add the following --

Erratum: "All the suffering animals will suffer No MORE but ..."
The greatness of a nation and its moral progress can be judged by the way its animals are treated—Gandhi.

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Re: The two-facedness of biology

Post by Theophane » January 5th, 2015, 4:57 am

"Pitiless Indifference" seems to be another way of expressing the idea of "Red In Tooth And Claw", I think. The only hope being no hope.

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Re: The two-facedness of biology

Post by Obvious Leo » January 5th, 2015, 5:26 am

The point that seems to be being missed here is that it is LIFE itself that evolves. The fate of its component parts is a trivial irrelevance, as good an argument against intelligent design as one could wish for. "Pitiless indifference" is an accurate enough description but an emotion-laden one. Applied to a self-organising system it is simply anthropomorphic and meaningless but applied to a creator god it is nothing short of barbaric. The god of the creationists is a sadist.

Regards Leo

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Re: The two-facedness of biology

Post by Misty » January 5th, 2015, 5:39 am

Obvious Leo wrote:
Mysterio448 wrote: So are you basically saying that the built-in sabotaging of the body is not an accident but is all a part of nature's plan? Like a biological fail-safe?
Exactly. I don't like the term "nature's plan" because of its teleological overtones but I don't think this is the sense in which you meant it. Nature has no plan. She just does what she does because she cannot do otherwise. The appearance of purpose is an effect rather than a cause. Only minds can have purpose.

Regards Leo
Then why would you call the workings of the universe including our bodies flawed and if created by a God that he/she was inept about it? "The appearance of purpose is an effect rather than a cause." dictionary meaning of effect: n. 1) result 2) meaning 3) influence 4) goods or possessions 5) vb: cause to happen. Purpose is built into nature. Nature is purpose in action.

-- Updated Mon Jan 05, 2015 4:40 am to add the following --

p.s. Minds observe nature/purpose.
Things are not always as they appear; it's a matter of perception.

The eyes can only see what the mind has, is, or will be prepared to comprehend.

I am Lion, hear me ROAR! Meow.

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