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雖然進化論者不斷否定進化論有甚麼問題，且強調科學家對進化論都不再存疑問，但事實上從科學證據而言，進化論還面對巨大困難。我最近讀了Casey Luskin的一篇文章，對進化論所面對的十大科學困難有詳細分析： “The Top Ten Scientific Problems with Biological
and Chemical Evolution.” [1] 這文章分析清晰，而且學術資料豐富，很值一讀。我們所出版的《智慧設計的當代爭論》對進化論的問題也多有論及，[2]然而所牽涉的資料汗牛充棟，我感到Luskin的文章仍然是很有價值的。[3]然而原文有數十頁，不易消化。因此，本文用中文作一些介紹和撮要，再加些少評語，期望讀者可以之後再細讀Luskin的原文。
十大問題概覽
問題一：沒有可行的機制去產生原始有機湯(Primordial Soup )
問題四：自然選擇難以把有利的特徵固定到生物群中
問題五：物種在化石紀錄中的突然出現並不支持達爾文式的進化論。
問題六：分子生物學並不能產生一個統一的宏大「生命樹」。
問題八：不同脊髓類動物的胚胎的差異與共同祖先論所預測的有衝突。
問題九：新達爾文主義難以解釋很多物種的地理分佈。
問題十：新達爾文主義關於退化器官(Vestigial Organs) 和垃圾DNA (Junk DNA) 的預測，在悠長的歷史中被證明是不正確的。
生物進化能發生的先決條件就是化學進化──第一個生命由無生命的物質產生的化學過程，而化學進化一個基本假設就是原始有機湯的存在。1953年，Stanley Miller與Harold Urey的實驗被視作原始有機湯的證據。然而：
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2010年，University College London的生物化學家Nick Lane承認原始有機湯的理論「不能成立」，而且「它已經過時了」。13他的新建議是生命是在海底的一些熱力出口(undersea
hydrothermal vents)中誕生的，然而在水中氨基酸和其他有機分子根本不會連結起來而產生蛋白質那類生化分子，這是National Academy of Sciences 也承認的。14相反，水的環境只會令蛋白質更容易分解為氨基酸。因此，化學進化是非常困難的。
究竟如何能由無生命的化學品跨越到第一個可自我複製的生命系統呢？現時一個流行的理論就是「RNA世界」。然而：
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從經驗看，沒有科學家有智慧地指導合成程序，RNA分子根本難以自動形成。
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RNA世界的理論不能解釋遺傳資訊的起源。. 第一個RNA大概需要200-300 nucleotides，但並沒有化學或物理定律可決定這些nucleotides的次序──但有正確的次序才能盛載遺傳資訊。18 進化論者能倚賴的只有機遇，但能隨機找到250 nucleotides的正確次序的或然率大概是1 in 10150 --這低於整個宇宙時空能產生的隨機事件。19 20
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這理論也不能解釋遺傳密碼(genetic code)的起源。單單有正確的遺傳資訊仍然與生命無益，我們必須能把遺傳資訊轉化為有功能的蛋白質，但這個轉化過程（如transcription、translation）本身又需要大量蛋白質和分子機器(molecular machines) ，然而這些蛋白質和分子機器的產生又是倚靠已經存在的遺傳資訊！這是一個雞與雞蛋的問題。
去解釋以上那點，Luskin使用了一個很好的比喻，就是第一個DVD與DVD機的起源。一隻DVD的確充滿資訊（如一套電影），但假若沒有DVD機把這些資訊轉化為圖像與聲音，它一點用也沒有。假設如何製造和使用第一個DVD機的說明書也只是紀錄在DVD中，那我們如何產生整個系統？答案很簡單：智慧設計能同時製造互相配合的DVD和DVD機。要有一個生命系統，不單要有正確的遺傳資訊，更要有轉化機制，而且兩者要說同一種語言！若不能發揮功能，自然選擇也無處著力。
2007年，哈佛大學化學家George Whitesides被頒授Priestley Medal──是美國化學家協會的最高榮譽，他發表演說時說：「生命的起源是科學的大問題之一，大部分化學家（包括我自己）相信生命是在無生命的地球的化學混合物中自然產生的。但如何產生？我一點頭緒也沒有。」22
生物擁有很多複雜架構，這也需要相應的複雜遺傳資訊，這些資訊真的能按照達爾文理論所言產生嗎？Lehigh University的生化學家Michael Behe指出：假若只須一個突變就能產生某種優勢，進化論面對的問題不大，但若需要多個突變才能產生功能優勢，那「進化」就只會陷於膠著狀態。24然而一個不可簡約的複雜架構需要多個組件同時存在才能發揮功能，所以要產生這些架構也需要多個突變，所以它們的產生是難以用進化論解釋的。
一個例子就是細菌的鞭毛(bacterial flagellum) --一個分子馬達(micromolecular rotary-engine) ，一些實驗顯示，只要缺少了約35個基因之一，它就不能發揮功能。32 Nature
Reviews Microbiology的一篇論文承認：「研究鞭毛的群體根本還未開始考慮這些系統是如何產生的。」33但生物的分子機器成千上萬，例如一個研究計劃就在酵母(yeast) 裡找到超過250個新的分子機器。34 不單這些分子機器往往有不可簡約的複雜性，製造這些機器的蛋白質本身也需要多個突變才能產生，這使問題雪上加霜。
有些批評者認為這些所謂低或然率難以量化，或只是建基於沒有實證的假設，然而這方面的實證生物學研究已有不少。2000和2004年，蛋白質科學家Douglas Axe在Journal of Molecular Biology 出版了他的實驗結果，指出一個能有穩定摺疊的蛋白質的或然率約是1 in 1074 ，那絕大多數的蛋白質根本就不能形成穩定結構，更遑論能發揮生物功能了。由於不同有功能的蛋白質有不同摺疊結構，那由一個有功能的蛋白質演化到另一個有功能的蛋白質，很難不經過一些沒有功能的階段，但這些階段卻會被自然選擇淘汰！[5]此外，在2004年，Behe與University of Pittsburgh的物理學家David Snoke模擬達爾文式的進化論如何產生蛋白質之間的互動，他們發現：若需要的是兩個或以上的突變，整個地球歷史用上也不夠時間。38
2011年，Douglas Axe 與Ann Gauger嘗試把一個細菌的酵素轉變為另一個相近的酵素，進化論者認為這類改變應該能輕易發生。然而他們發現這改變最少需要七個同步的突變──而這超越了地球歷史能產生的極限。40 以上那種改變雖然相對簡單，但已是這麼困難，那更複雜的改變就更不可能了。Gauger與University of Wisconsin, Superior的生物學家Ralph Seelke做了另一個實驗，他們故意破壞了大腸杆菌製造氨基酸tryptophan的基因。他們發現，若破壞只限於一點，那細菌的確能透過隨機突變修復這基因。然而若被破壞的點超過兩個，那達爾文式的進化根本不能令細菌重拾功能。41
問題四：自然選擇難以把有利的特徵固定到生物群中
2008年，16位來自世界各地的生物學家在奧地利的Altenberg開會，探討進化論的問題。科學期刊Nature也有報道這"Altenberg 16"會議，引述一些著名科學家說：「翅膀的起源和生命的登陸. . . 等事情，進化論能告訴我們的非常少。」49我們姑且假設一些突變能產生一些有利生存的新特徵，但若要達成生命的進化，這特徵還要固定到生物群中。進化論者經常假設這是輕如易舉之事，但在真實世界卻沒有那麼簡單。例如一些活在冰天雪地的狐狸本來的毛是棕色的，但後來一隻演化出白毛來，應該是有掩護作用的。然而有很多意外可能發生，例如這隻白狐狸可能斷了腿或被吃掉，那牠的有利基因就不能傳遞下去。所以，不少隨機力量（通稱為遺傳飄移[genetic drift]）能輕易把有利突變取消，除非這新特徵帶來的優勢非常巨大。如Indiana University的進化生物學家Michael Lynch說：「隨機的遺傳飄移對分子的改良是強大的障礙。」50 遺傳飄移甚至傾向把一些中性或輕微不利的突變固定下來。51 Lynch指出很多進化論者把自然選擇描繪為一種無所不能的力量，能產任何生物的複雜結構，他卻認為這是神話。56 58Lynch則相信隨機的遺傳飄移才是主要的解釋，但這種觀點又受到嚴厲批評，如Ann Gauger，59 和進化論者Jerry Coyne。60看來雙方的批評都有道理，無論是自然選擇或遺傳飄移都不能充分解釋生物複雜性的產生。
達爾文預期化石紀錄應該充滿著物種與物種之間的中介生物，但事實並非如此，所以他在《物種起源》裡也問：「為何不是每一個地質岩層都充斥著這些中介連繫呢？」 66他承認這是進化論要面對的最大問題，而他那時的解釋是訴諸化石紀錄的不完整。然而150年過去了，今天數以千計的物種在化石紀錄中被發現，只有很少數看起來像中介生物。如古生物學家Stephen Jay Gould承認：「在生物設計的主要轉接之間的中介階段，我們並沒有化石證據；事實上在很多情況下，就算在我們的想像中去建構一些功能上中介的生物也很困難，這一直是漸進進化論持久面對的嚴重問題。」68
絕大部分生物都是突然出現，沒有明顯的祖先，而且出現時已相當完整，之後也沒有巨大變化。一些例子如下：
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有關人類的演化，著名進化生物學家Ernst Mayr在2004指出：「在Homo, Homo
rudolfensis和Homo erectus的最早化石，與及Australopithecus之間，存在一個巨大且沒有連接的鴻溝。我們如何解釋這個表面的跳躍呢？…並沒有可視作缺環的化石。」92
按進化論的假設，不同物種的生化分子是由祖先漸漸演變而來，所以比較它們相似的程度，應當可以決定他們在演化的系譜上有多接近，這樣就可建構代表演化過程的「生命樹」。生物擁有多種生化分子（如蛋白質、DNA等），但真實的演化過程只有一個，所以我們也可預期，使用不同生物分子去建構的生命樹，大體上也應互相吻合的。然而事實卻非如此，如New Scientist所言：「長久以來建構生命樹就是[生物學家] 的聖杯…但今天這個研究計劃已是頹桓敗瓦，被相反的證據撕成碎片。」104
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當這種矛盾在細菌上出現時，進化論者提出基因交換(gene-swapping)
的機制去解釋。然而這類矛盾在較高等的動物中也出現，但牠們之間不多出現基因交換。當微生物學家Michael Syvanen研究不同動物的2000個基因，企圖建構牠們之間的演化關係，但他失敗了，因為不同基因所說的故事互相衝突，不能協調。107到最後Syvanen哀嘆：「我們剛剛殲滅了生命樹了。」108
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一般生命樹認定人與rodents較接近，與大象則較疏遠。然而microRNA基因的分析卻顯示人其實與大象較接近，這類建基於基因比較的生命樹的衝突比比皆是。Dartmouth的生物學家Kevin Peterson說：「我研究了數以千計的microRNA基因，但我找不到一個支持傳統生命樹的例子。... 它們提供的生命樹與所有人希望見到的都截然不同。」111
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就算在同一個物種的基因內，我們用不同基因去建構的生命樹也互不相容。使用不同蛋白質得出的結果亦是互相矛盾。
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除了使用分子分析外，我們亦可透過比較生物的形態(morphology) 去建構生命樹。但兩種方法得出的生命樹亦是經常發生衝突。且是資料愈多，衝突愈嚴重。112例如進化論者經常提到使用酵素cytochrome c所得出的生命樹，與建基於形態的傳統生命樹相當吻合，但其實若建基於cytochrome b，則會得出於傳統生命樹截然不同的結果（如貓與鯨魚都被歸入靈長類），114他們對此卻隻字不提。
面對這些矛盾，進化論者提出了不少臨時的解釋：horizontal gene transfer, long branch attraction, rapid
evolution, different rates of evolution, coalescent theory, incomplete
sampling, flawed methodology, and convergent evolution，但或許要質疑的是生命樹背後的基本假設，就是所有生物都有一個共同祖先。
進化論的一個基本假設，就是生物的相似性反映了來自共同祖先的遺傳資訊。然而我們發現在不少情況下，當兩個物種有一些相似特徵時，這特徵是不可能源自牠們的共同祖先的，這被稱為趨同進化(convergent or parallel evolution)。然而這也意味著，生物的相似性不一定反映共同祖先的遺傳，這即是說進化論的基本假設不是完全正確的。
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科學家研究不同物種的粒線體DNA(mitochondrial DNA, or mtDNA) ，發現一些鳥類的mtDNA與一些疏遠的物種（如蛇與蜥蜴）的mtDNA相當相似，看來這些mtDNA是有「多次獨立的起源」。120
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其他趨同進化的例子包括：眼睛的多次出現；脊髓類動物的色素改變；蛋白質的特質；mimicry in butterflies for mutualistic interactions；convergence of some flower traits
in plants等。125
問題八：不同脊髓類動物的胚胎的差異與共同祖先論所預測的有衝突。
進化論者認為，不同脊髓類動物的胚胎發展有巨大相似之處，這與共同祖先論所預測的一致，所以可成為進化論的證據。然而當生物學家經過仔細研究，發現不同脊髓類動物的胚胎發展從最早階段開始就存在差異，與共同祖先論所預測的有所衝突。130 131 132
一些進化論者仍然堅持在一個中間的階段，不同脊髓類動物的胚胎呈現高度相似性，這被稱為phylotypic stage。然而Anatomy and Embryology 的一個全面研究指出這也不正確，因為那些胚胎在以下幾方面都存在不少差異：身體的大小，身體計劃(body plan) 、生長規律和發展時間表。134
生物地理學(Biogeography)
被視為支持進化論的重要證據，然而很多不符的例子卻被忽略了：
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南美洲有一種猴子叫platyrrhines，根據形態和分子的分析，進化論者認為牠們是非洲猴子catarrhine的後裔。化石紀錄顯示猴子在南美洲生存了約三千萬年，但地質證據卻顯示南美洲與非洲在一億年前已經分開。137 那究竟非洲的猴子是如何橫渡廣闊的海洋（兩者之間相距程最小2600公里），去到南美洲再演化出新的猴子物種的呢？這實在是一個大難題。140
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一些科學家提出猴子是乘木筏飄洋過海的，但這可能性又多大？而且一定要有兩隻猴子一同渡過，旅程所需的食物和食水又從何而來？這些理論的牽強，實在令人嘆為觀止。我們亦可提問：若飄洋過海這麼容易，為何其他非洲靈長類沒有去到南美洲繁衍，而只有猴子呢？
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其他例子還有：南美洲的蜥蜴和large caviomorph rodents；Madagascar的密蜂、lemurs和其他哺乳類；150 很多海島中出現的大象化石；151 橫跨海島鏈出現的淡水青蛙。152
1925年，進化生物學家Horatio Hackett
Newman認為人體中有超過180個退化器官，但隨著日子過去，一個又一個的「退化器官」的功能和目的都被發現。New Scientist 在2008的報告指出今天「生物學家根本非常害怕談及退化器官。」158 進化論者又把這種思維應用到基因上，因為只有2%的人類基因是用來製造蛋白質的，他們就認為餘下的98%大多是垃圾基因，是進化歷程的遺物。 然而今天很多所謂「垃圾基因」的功能已被找出來。
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人類基因中有一些不斷重覆的元素，一直被認為是「垃圾」，然而生物學家Richard Sternberg在Annals of the New York Academy of Sciences指出，這些重覆DNA(如SINE)的功能包括：形成更高層次的細胞核結構、centromeres和telomeres等；協助細胞繁衍；基因的翻譯；DNA修補等。168
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各種不牽涉於製造蛋白質的DNA的功能包括：修補DNA；174 協助DNA複製；175 規管DNA的transcription；176 協助染色體的摺疊和維持；177 控制RNA的編輯和切開；178 協助抵抗疾病；179 規管胚胎發展。180
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2012年，Nature報道了一個多年的研究計劃叫ENCODE ，超過400個科學家參與其中，他們的目的就是研究不牽涉於製造蛋白質的DNA的功能。ENCODE的主要報告說：「這些資料讓我們能指定80%的基因庫的生化功能，特別在那些製造蛋白質的區域以外的DNA。」182事實上ENCODE 只研究了147種細胞，但人體擁有數千種細胞，所以有功能的DNA「可能會超過80%，而達到100%。」183
當然，我們還未完全明白基因庫的功能，但現在科研的趨勢是：我們愈仔細研究所謂「垃圾基因」，我們愈加發現它們的功能。其實「垃圾基因」的概念源自達爾文式的進化論，在過往幾十年是生物學的主流範式(paradigm) ，很多生物學家都不敢質疑，所以只有少數科學家去研究它們的功能。由此看來，進化論的框框實在窒礙了生物學的發展。
結語
當然，進化論的爭論是異常複雜的，所以我無意說單憑以上資料，進化論已被百分百否證。面對以上的難題，進化論者也會提出多種解釋和回應。這些回應是否足夠，還須深入探討，然而坊間往往對進化論的問題缺乏認識，而一些「護教學家」對進化論的批評則有時流於表面，所以我希望能介紹一些有扎實學術基礎的批評，一方面突破一些進化論者製造的假象，另一方面也要提昇批評進化論的論述的質素（參以下的學術參考資料）。我多年來對這問題相當關注，也相信以上進化論的十大問題的確令進化論的可信性大幅減低，然而我們在提出這些主張時，應堅持學術和理性的態度，我們還需要做的工夫有很多。
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[1] 見http://www.discovery.org/a/24041，這文章收集於Robert
Stackpole and Paul Brown, eds., More than Myth (Chartwell
Press, 2014).
[3] 另參Michael Denton’s Evolution:
Still a Theory in Crisis (Seattle
[6] 有關這方面的研究和爭論，可參Stephen
Meyer’s Darwin’s Doubt: The Explosive Origin of Animal Life & the Case for
Intelligent Design (New York: HarperOne, 2013)，他在此書中批判地檢視了進化論者對寒武紀大爆炸的諸種解釋，也引起了不少爭議。Meyer及其盟友也作出了回應：David Klinghoffer, ed., Debating
Darwin’s Doubt: A Scientific Controversy That Can No Longer Be Denied (Seattle: Discovery Institute, 2015) 。
