在生物學上如何決定一個器官的功能﹐是一個具爭議性的課題﹐這涉及如何分辨運作正常或失靈。心臟的功能是泵血﹐但發出啪啪的心跳聲﹐又算不算心臟的功能呢﹖如果一個人的心臟能夠泵血但不會發出心跳聲﹐他的心臟又算不算運作正常呢。在近代生物學的傳統﹐生物的各個器官的功能﹐可以用進化論去解釋﹐從物競天擇適者生存的定律﹐去推論什麼是器官的功能。任何器官的功能﹐最終也是以增加生存或繁殖後代的機會為準則。心臟若果不能泵血﹐生物便會死亡﹐所以泵血是心臟的功能。但心跳聲並不會增加進化優勢﹐所以那便不是心臟的功能用。

用這個說法去解釋生學的功能有一個問題﹐就是沒有辨法定義與無關進化的生物或器官的功能。例如人類解剖到外星人﹐人類並不知道外星人如何進化﹐那便無從決定外星人器官的功能。又例如X-Men漫畫裏的Cyclops﹐他的眼睛可以射出激光﹐可是那個能力是因為基因突變﹐並不是從物競天擇進化而來。根據這個功用源於進化的定義﹐射出激光並不是Cyclops眼睛的功能﹐但這個說法明顯地十分荒謬。這篇功課便是探討生物學上功能的定義﹐並提出能夠應付上述情況的新功能理論。

What is function in biology?

Abstract: In this paper, I am going to argue Prior’s account of functional analysis is most promising theory of function in biology based on the selected important desiderata for a theory of biological function. I will then defense Prior’s view against Neander’s attack from the prima facie problem with teleological explanations.

In the second half of the course, we have surveyed many accounts on theory of function in biology. Namely we have studied a few rejected classical theory of function in [1] and [2], the standard etiological approach proposed by Wright [1], the system approach proposed by Cummins [2], the goal oriented approach proposed by Boorse [3], the forward-looking approach proposed by Bigelow [4] and the functional analysis approach proposed by Prior [6]. Neander’s paper does not make any new proposal but rather fortify the Wright’s argument. Godfrey-smith’s paper spoil the fun of the party by proposing that the two major camps in this debate, Wright and Cummins respectively, are talking about two different notation of functions. Out of the all the functional theory, I think Prior’s account that is based on a modified Cummins approach is the most promising approach to explain what is function in biology. I will first summarize the desiderata for a theory of biological function by collecting all the functional criteria from all the papers.

An acceptable account of theory of biological function must able to answer the following questions:

1. An acceptable functional theory must distinguish between function and merely effect. For example, the heart’s function is to pump blood; its function is not to make throbbing sound. This example is used by both Wright and Cummins. This is pretty much one of the most fundamental acid test for any functional theory.

2. An acceptable functional theory must explain both artificial (conscious) and natural (biological) function. Actually in my opinion, throwing away this criterion will open up all the limitation of biology functional theory. If we can treat artificial function and natural function as two distinguish and non-intersecting categories, most of the argument in functional theory will simply disappear. Biological function will become much like physical function and chemical function that is just a descriptive account of the causation effects and what happen as it is. However Wright, Cummins and pretty much everyone else choose to keep the criteria, I have to include it in this paper to keep the premise consistence with all the papers

3. An acceptable functional theory must distinguish function from malfunction, non-function, vestige, statistically normal function, accident and unintended function. This criterion is where the different functional theories disagree with each others, in another word this is the heated battle ground. The Cummins camp attacks the Wright camp that the etiological approach cannot deal with any one of those distinctions or all of the above. The Wright camp defenses the etiological theory by counter argue that their account can handle the distinctions. One problem I observe is that the actual meaning of function seems twisted one way or another by each camp to fit their functional theory. Here I will propose an acid test for each type of distinction to keep the criterion simple. A heart that cannot pump blood, say there is some genetic defect and the heart is born with a missing a valve, is a malfunction heart. An appendix is a non-functioning and vestige organ in human. If a virus causes 99% of the population to go blind, the function of an eye is still to see. The function of a belt bucket is not stopping bullet, although sometimes accident does happen and it does stop bullet and saves life. The function of Prior’s hypothetical grape-prawn peeler is to shell prawn. Alternatively, we can substitute a real world example for the grape-prawn peeler. When laser was invented, it was intended be used as laser weapon, but it turns out laser also is very useful in reading data from DVDs.

4. An acceptable functional theory must take into account of super function. Here is an example of super function. Normally the function of an eye is to see. However in the comics X-Men, Cyclops, a mutant superhero, can shoot laser from his eyes. Therefore function of his eye is both seeing and shooting laser. Yet we do not know whether shooting laser from eyes has any evolutionary advantage or even an inheritable genetic trait. The comics do not mention he has any offspring and just the fact of being a mutant always puts his life in great danger. In the next section, I am going to outline Prior’s functional theory and contrast it with Wright’s etiological theory. I will examine both theories base on the desiderata defined above. Prior’s define function statement as the output of functional analysis. “According to this account the ascription of a function is both theory and interest relative – the function of a particular organ will be that of its effects which features in our best account of some interesting (higher-level) capacity of the organism in question.”[6] He also said that his account is familiar similar to Cummins’ functional analysis that “functions are appealed to in order to explain the capacities of their containing systems, and not the existences of the item to which the function is attributed.”[6] In contrary, Wright’s etiological account states that “The function of X is Z means: (a) X is there because it does Z, (b) Z is a consequence (or result) of X’s being there” [1] In short, Prior’s theory does not care about how the organ comes into place, it only cares about the effect and relationship between the organ and the organism or the organism and the ecosystem. On the other hand, Wright’s theory requires the function to explain how the organ comes into place.

Both Prior and Wright’s theory easily pass the first criteria although they have different explanation. In Prior’s account, he can follow Cummin’s explain the function of heart under the context of the blood circulatory system. Since the pumping of blood but not making the heart beating sound is a desired effect of the heart in the circulatory system in explaining its capacity, we can distinguish the function of the heart as pumping blood against making noise is merely an effect. Wright would explain the function of heart by stating that the heart pumping blood gives evolutionary advantage to the species hence increase the fitness to survival for those who population within the species who process this genotype, as a result a blood pumping heart exists because that is what was selected for. The heart beating sound does not give any evolutionary advantage, it is a selected of, a trait merely got inherited tagging the tagged along with the pumping function of heart. Since the first criterion is the most basic requirement of any functional theory, I am not surprised both theories can explain it well.

The second criterion is does not have much controversy since both Prior and Wright deliberately took the effort to make their theories compatible with artificial selection. Prior’s approach actually originates from functional account of artificial function and extend it to cover natural function. The function of a mechanical part is determined by its design intention within the mechanical system. In the pre-Darwin where creationism rules the study of nature theory, natural function pretty much share the same account as artificial function. The only difference is the conscious agent for artificial function is human and the conscious agent for natural function is God. Medieval doctors explain biological function in term of physiological function which a result of the functional analysis procedure for the whole body. However this account is not without problem. By definition no one know the real intention of God, so the natural function is really only based on what people’s guesses about God’s intention or on powerful religion figure’s claim on knowing the intention of God. If the intention is not known or incorrect, the function could be totally wrong. For a long time in the history, people think generating emotion is also a function of the heart, which is obviously wrong under the light of modern science. Wright’s approach is the opposite; it extends the biological account of natural function to cover artificial function by replacing natural selection with the selection by the designer or user. In this sense, it actually simplifies the problem of the etiological account. The biggest problem of etiological account is base on the natural selection theory which it is somewhat questionable as we learn in previous lectures. Replacing natural selection with an artificial selection originated from a conscious agent eliminate the uncertainty in the equation. If there is any doubt, we can always get clarification by asking the agent for his selection criteria.

Prior’s theory does not have much problem with the third criterion. Once the nominal function is identified through functional analysis in the context of the system and its capacity, any derivation from the nominal function can treat as malfunction, non-function or accident. If the system changes and the nominal function are no longer required, it becomes a vestige. If the context of the system and its capacity is indentified correctly in related to a higher level system, we can deduce the intention of the function and figure out the difference between the statistical normal function and the nominal function. Unintended function can be deal with by a running a new functional analysis after updating the context and capacity of the system. Wright account has a harder time answering the question posed by the third criterion. Malfunction and non-function can be understand in the relationship of token and type, deviations from of token from the type that lower the fitness can be seen as a malfunction or non-function. Vestige is the easiest to deal with since the etiological account keeps track of the historical record of the function. Statistical normal function is a bit harder to deal with using the backward looking account, but if we patch the etiological theory with Bigelow’s [4] forward looking account, we can still distinguish between function and statistical normal function. For example, a virus that blind 99% of the population would not change the function of the eye, because having an eye that can see still have an evolution advantage. In the etiological account if a function is not inherited then we can treat it as an accident instead of a function. Backward looking account cannot deal with unintended function, but it has no problem in the forward looking account since unintended function is still a function as long as it has a selective advantage.

I believe the forth criterion really sets the two theories apart. According to the comics, Cyclops acquires the ability of laser eye due to first generation genetic mutation. Clearly there is no previous selection history Wright can use in the backward etiological account. Having a laser eye does not make him more attractive to women, so it does not give him any reproductive advantage. In the world of X-men, the government hunts down mutants, the evil mutants launch a war on the good mutants for world domination and occasionally the good mutants have to defense the Earth from alien invasion. Mutants seem to have a worse survivability compare to the normal people. If there is no forward selection advantage, we cannot use Bigelow’s forward etiological account. However, it would be odd to say shooting out laser is not a function of Cyclops’ eyes because that’s what they really do. Prior’s account has no such problem, we can examine Cyclops as mutant, which is a different system compare to normal people. We can easily perform functional analysis on his eyes and concludes they have the function of seeing thing and shooting lasers. This approach is exactly how the medieval doctors determine the function of human body parts and the X-File scientist in Area 51 figure out functions of alien body parts when they dissect the alien.

In Neander’s paper [5], she argues against Cummin’s account following a different strategy. She employed the prima facie general problem concerning all teleological explanations which explains the means by the ends; a development or trait is explained by reference to goals, purposes of functions. Teleological explanations appeals to the effects but it is often that the purposes, goal and functional effects are never realized. In the case of artificial function, instead of appeal to the actual effect of the function, the teleological explanations appeal to the intended effect of the agent. When the purposes go unfulfilled, the agent still has a purpose. Clearly, the explanatory power of purposive explanations does not derive from their explicit reference to future effects so much as their implicit reference thereby to past intentional attitudes to those future effects. In short, teleological explanations are just a species of ordinary casual explanation. The problem with biological function is there is no intentional agent. Prior cannot appeal to God nor Mother Nature’s intention or evolutionary design, since those misguided pseudo-explanation are not scientifically respectable.

In Prior’s paper, he sort of response to the teleological problem by stating that it is just a “fundamental fact about human beings (or animals, plants, insects) that they are highly interested in survival and reproduction.” [6] He dodged the theological question of the ultimate intention by simply assuming it is a fact. He also stated that the ultimate purpose of biological life from is contagious by citing an example of an imaginary world with human life form wish to die happily instead of survive and procreate. I am not very please with Prior’s defense since his defense is pretty weak. He is just making a groundless assumption about human nature or biological life form in general. I can already contradict his idea about human purpose with any major religion beliefs. For example: to Christianity, the purpose of human being is not to survive or to reproduce; rather it is to go to heaven; to Buddhist, the purpose of human being is to reincarnate and reach nirvana.

I am going to response Neander teleological problem by using the human centric view that stating it is us, the human being, gives purpose to the nature. Nature may not have any purpose by itself; but that does not mean human cannot assign some purpose to the nature. At the end of the day, it is human, neither God nor Mother Nature, is where the conscious agent that all the teleological intention ends. With the advance of modern science, like genetic engineering, geo-engineering, climate control, space colony, human will eventually has the power to shape the nature to the way we want. There will be no natural intention, everything is artificial intention. For the time being, natural intentions are merely artificial intention that we haven’t figure out a way to control yet. To summarize, the function of an egg to a chicken is a mean to reproduce. The function of an egg to human is breakfast, and the function of a chicken to human is lunch or dinner. Prior’s account is the most possible explanation for function, my minor twist to Prior’s account is human is in the center of all system, so we are the conscious agent and eventually nature function will be mostly equivalent to artificial function, except that nature function is generated by evolution engineering.

References:
1. Wright, Larry (1973) “Functions” Philosophical Review. Vol. 82, pp. 139-68
2. Cummins, Robert (1975) “Functional Analysis” Journal of Philosophy. Vol. 72, pp. 741-64
3. Boorse, Christopher (1976) “Wright on Functions” Philosophical Review. Vol. 85, pp, 70-86.
4. Bigelow, John, and Robert Pargetter (1987) “Functions” Journal of Philosophy. Vol. 84 (4), pp. 181-96.
5. Neander (1991) “The Teleological Notion of ‘Function’” Australasian Journal of Philosophy.
6. Prior (1985) “What is Wrong with Etiological Accounts of Biological Function?” Pacific Philosophical Quarterly.
7. Godfrey-Smith (1993) “Functions: Consensus Without Unity” Pacific Philosophical Quarterly.

進化論的其中一個很多爭議的問題﹐是達爾文提出物競天擇適者生者這個大自然定律﹐不能解釋物種如何進化出某些基因特質。例如生物學家用進化論﹐如何能推論出人類的姆指是從何進化而來呢。哲學家Sober提出一種說法﹐認為進化論根本不能解釋物種如何進化出某些基因特質。進化論應該要反過來解讀﹐去解釋沒有某些基因特質的其他物種為什麼絕種。物種從基因突變產生新的基因特質﹐大自然定律淘汰了不適合生存的基因﹐剩下來的基因便是能夠存活並繁殖後代。另一哲學家Neander則提出相反說法﹐說因為基因轉變有累積性﹐進化論可以解釋物種基因特質的變化。其實這個爭議有點無聊﹐在我看來不過是雙方在咬文嚼字﹐大家對進化論中因果關係的定義沒有共識﹐才會有這個有點牛頭不對馬嘴的辯論。

Does natural selection explain why you and I have opposable thumbs?

In the debate between negative and positive natural selection, Sober argues that natural selection does not contribute to the existence of individual traits within the population. Neander argues that the cumulative natural selection process shapes the genetic properties of the population. Nanay backs up Neander’s claim and argues both arguments do not take limitation of environment resources in the account. In this essay, I will further enhance Nanya’s argument by stressing how direct competition over resource among individuals with different traits can be affected the process natural selection. I will present an argument that cumulative selection process could decisively alter the genetic trait of the population in the presence of direct competition; thus explain the why you and I have opposable thumbs.

In [1], Neander summarize Sober’s argument for the negative view of natural selection. Sober argue that natural selection cannot explain why you and I have opposable thumbs, natural selection can only explain why all our distance cousins without opposable thumbs are eliminated by natural selection. The negative view states that natural selection cannot create new traits; it can only destroy traits that are not fit for survival. The traits of individual either come from inheritance or random mutation. Natural selection did not create the tree of life: it just determines which branches were removed and which remained. [1, p68]. Sober illustrate the negative view of natural selection using an example of a class of third grade students who can read and write at the level of third grade. Every student in the third grade class can read and write at the third grade level because that is exactly the selection criteria of the class. No student who cannot read or write at third grade level is selected into the class in the first place. Therefore, merely the fact that the student is in the third grade class does not explain how each student acquires his reading and writing skill.

In [4], Walsh makes a distinction between two types of explanations national selection, the wide scope and narrow scope. The wide scope explanation explains the frequency of traits within a population is biased by cumulative selection. The narrow scope explanation explains why a given individual possesses a particular trait. Walsh agrees with Neander that natural selection is two-stage process by taking into account of the reproduction factor. In the first stage, the new traits from random mutation are selected to pass down to the offspring. The second stage then has a biased population base to start the next iteration of reproduction. Traits that affect reproductive success will cumulatively alter the population make up in the long run. Walsh argues that the two-stage process only address the wide scope explanation by answering how a trait type is arise within a population from the selection advantage of that trait, but it does not answer the narrow scope question that explains how the trait token occurs in each individual of the population.

In [5], Nanay tries to address the narrow scope question by bringing in another factor into the equation, namely the limitation of resource in the environment. Nanay argues if individuals with different traits are compete for the same environment resources and the total population the environment can support has a limit, then elimination of individuals of one trait alter the chances of survival of other individuals with a different trait. The trait is more fit to survive in the competition of scare resource will have a selection advantage. In short, the distribution of different traits within the population is a zero sum game. The adaptation of one trait is in the expense of another mutually exclusive trait that is inferior in term of survival fitness. The elimination of the later trait is the other side of the same coin of the survival of the former trait. Nanay provides an indirect explanation to the narrow scope question by making the claim that individual with a certain trait exists because its parent with the same trait survive and reach reproductive age thanks to other individual with a different trait in the previous generation failed to survive and reproduce.

In this long debate started by Sober and Neander, we can observe a trend that is going on. The negative view camp first posed a question that cannot be answered by natural selection. The positive view camp counter attack by introducing new parameters into the equation of natural selection and claim there is a causal relationship between the survived trait is the selected trait. For example, Neander introduces the reproduction factor and Nanay introduces the limitation of environmental resources. The negative view camp defense by narrowing the definition of the natural selection question and focus on how the the inheritance linage of an individual occurs. I am not satisfy with Nanay’s indirect explanation because there are still rooms for the negative view camp to further narrow down the natural selection question and dodge the bullet. The elimination of trait B does not necessarily imply the inheritance of trait A, given that there are numerous other traits out there that are also completing for survival. I would like to introduce a parameter into the natural selection equation and seal the escape route of the negative camp once for all. The new parameter I would like to introduce is direct competition of reproduction of individual with different traits within the population. Nanay argues that indirect competition of scared resource in environment for survival and reproduction can indirectly explain why how a particular trait arises in an individual. Then the trait contributes to the direct competition of reproduction and survival can directly explain how a particular trait arises in an individual. Let me illustrate what direct competition is with a real world example, the moose horn. Male moose fight using their horn for the right to mate with female moose. Suppose in one generation, there is a random mutation of the moose horn genes and create two different genetic traits. Trait A is the normal horn gene that grows horn with regular strength. Trait B is the super horn gene that grows much stronger horn. The individual with super horn gene will win the fight and able to mate and reproduce offspring. Those offspring with super horn gene will further displace the normal horn gene in the next generation. By applying mathematical models, given that the survival fitness of individuals with the super horn gene is equal to individuals with normal horn gene in all other aspect, the super horn gene will spread over the entire population following the equation geometric series. In the case of direct competition in reproduction, we can answer the narrow scope question decisively. Individual trait token is inherited because the trait token has a reproduction advantage in the population. The other trait token lose the reproduction completion to this trait token in the previous generation. Instead of explaining the natural selection in terms of how the survival of the fitness affect probability distribution of trait token in the population, my explanation explains the inherence linage of individual traits in a winner takes all survival games.

Let me illustrate my explanation further by going back to Sober’s classic analogy of a third grade class. In Nanay indirect explanation, there are limited seats in the third grade class, only students who passed the second grade can be promoted to the third grade. The twist is the mark scheme of the exam uses bell curve to determine who pass and who fail. Those at the bottom of the class that failed the second grade exam are equivalent to those individuals with traits do not survive to reproductive age. It is arguable that the indirect explanation still does not explain how each student in the third grade class acquires their third grade reading and writing ability, rather it is the third grade reading and writing standard is adjusted to meet the ability of last student who barely survive the exam cut off threshold. In my direct competition explanation, it is not a typical third grade class. It is a third grade class in a ninja assassin school. The ninja assassin school does not teach reading or writing, rather it teaches killing and self-defense. The second grade exam is not a pencil and paper test, it is literally a fight for survival. The second grade students are put inside a huge boxing ring and asked to have round robin fights using their best killing or self-defense skill. Those who remain standing at the end of the exam period got promoted to the third grade. It is irrelevant how the students acquire their killing or self-defense skill prior to the exam, because only killing or self-defense skill matter in the selection process.

In my conclusion remarks, I am drawing the significant of opposable thumbs in the direct competition of reproduction and survival. It is evident that without opposable thumbs, human cannot use tools and more important weapons. Imagine there are two tribes of pre-historical human; one tribe developed an opposable thumb while the other did not. For the first few millenniums before human invent stone tools and weapons, the opposable thumb did not give the former tribe neither survival advantage nor disadvantage. The two tribes populate the environment and multiply with roughly the same rate. Yet the balance of power is tipped once the tribe with opposable thumb developed tools and weapons. With the help of tools and weapons, the former tribe is able to genocide the later tribe when they are fighting for the control of the land. Having the opposable thumb and the ability to use weapon is a decisive winning factor in pre-historical warfare. Since the ancestors of our non-existed distant cousin without opposable thumbs are killed by our ancestors who have opposable thumbs, natural selection explains why you and I have opposable thumbs. Survival of the fitness does not only explain the survival of a particular genetic trait in relationship to the environment, it also explains the survival of a particular genetic trait in relationship to other traits. Natural selection is not a marathon that let all the traits develops on its own and then figure out which trait pass the finishing line first. Natural selection is like the Stanley cup play off, it makes different traits play head to head against each other and let the fittest traits be the winner.

References:
1 . Neander (1995) “Pruning the Tree of Life” British Journal for the Philosophy of Science. Vol. 46, pp. 59-80.
2 . Sober (1995) “Natural Selection and Distributive Explanation: A Reply to Neander”, BJPS. Vol. 46, pp.384-397.
3 . Neander (1995) “Explaining Complex Adaptations: A Reply to Sober’s ‘Reply to Neander’”, BJPS. Vol. 46, pp. 583-87.
4 . Walsh (1998) “The Scope of Selection: Sober and Neander on What Natural Selection Explains” Australasian Journal of Philosophy. Vol. 76 (2) pp. 250-64.
5 . Nanay (2005) “Does Cumulative Selection Explain Adaptation?” Philosophy of Science, Vol 72, pp. 1099–1112.