Category Archives: 生物科学 BioScience

Dr. Andrew Weaver’s Talk on Climate Change

I went to Dr. Andrew Weaver’s talk on climate change, well, in fact about how climate change was communicated. It was an inspiring talk, and totally explained why people living in North America, especially the US, do not believe global warming or climate change.

Essentially, first, there are special interest groups. And special interest groups probably influence politics. A strategist once wrote a memo to the GOP basically saying that they need to make sure people believe that the global warming is uncertain among scientists, by somehow let scientists and engineer to say it for them.

Second. US media/journalism like to do “balanced” reports. They state some facts first. And they interview scientist who say the temperature is indeed rising. Then they interview other people who oppose global warming or deny human contribution. These people probably are totally not credible at all when examined by scientific peer review standard. About 50% and 70% reports between a studied 5 year period or so, on newspaper/magazines and TV, are these “balanced” reports. No wonder Americans are so confused! But this is not the first time nor the only case where media can sway public opinions.

Third. The special interest groups are still working. Rumors were spread ahead of Copenhagen meeting. And he expect more coming this year because of ad hoc or UN meeting in Bonn and Mexico this year. And yes people confuse more snow last winter with global warming is probably hoax.

I am not going to reproduce all of his talk and it is also impossible.

But what’s interesting to me, is that although we know US media hate global warming, the conservative party and people hate it, US media still give it 50-70% “balanced” reports which supposedly present opinions from both sides.

From my nonscientific perception, reports about China are about 20-30% “balanced”. Apparently they hate China more than global warming.

It’s the trust issue between US and China. And trust cannot be earned when there are no basis for it. Unless there are a lot of underground negotiation we are not aware of. But without both countries’ involvement, stop global warming is like… impossible.

Obama never takes responsibilities…

Although he claims that Afghanistan is the right battlefield instead of Iraq and he became a committee in the senate on such issue, he has never hold any hearing, and in this video, he excuses himself as too busy running for the presidential campaign.

Also in this video, he said he has “news” for McCain: if Bush and him never started war in Iraq, there will be no Al-Qaeda in Iraq. Again he got huge applause in the audience. Like before, what he said is true but that does not support his opinion. Guess that’s why CNN reporters in the video said this does not make sense. I have a feeling that Obama fans applause for anything without really thinking through. It is just like a cult, or cultural revolution in China.

Enjoy the video.






广电总局延长禁播境外制作动画片时间一小时. 也许可以禁用境外研制科技产品,这样我们的科技肯定飞黄腾达.

Is James D. Watson a Racist?

James D. Watson, nobel prize winner for discovering DNA double helix structure, seems to be good at making controversial comments.

Recently he has made comments about how geographically separated races may not have evolved identically, and he was inherently gloomy about the future of Africa. He tends to believe, the intelligence of difference races are not the same, and Blacks may not be the same intelligence as ours (the white).

Apparently this kind of comments are not politically correct in America, in which racist is more of a problem due to the fact of mixed race society. However, I believe Dr. Watson, and other scientists should be entitled the rights to do research on the following issues:

  • Whether difference races show different brain activities depending on the task they are assigned to do, and whether the results have genetic basis?
  • Whether there is connection between these above finding and the history of difference races?
  • If there are differences between races, what does that mean for our world, and what should we do about it on the basis that everyone is equal?

These research are pure science and should NOT be considered racist, although racists could use these findings as reasons for them to be racist. For people who are not doing science, which means pursuit of truth with scientific methods, it may be difficult to understand why we should do science which seems immoral or politically incorrect, and probably that’s why many scientists would not talk about these issues. I believe Dr. Watson is a brave man to talk about this, although he may have done it in an inappropriate way.

Although no strong evidence to support Dr. Watson’s “hypothesis” at this moment, it is not proved wrong either. Science is about proving something is wrong, and accept the rest “correct” as facts because there is no evidence to show it is wrong. Whether different race have different brain activities at the level of molecule, is something can be tested and proven. Whether they act differently for different tasks, can be proven too.

We have accepted physical differences between races. Black can do sports better. We agree Blacks can do music and dance in a much more different way than other races. It is even accepted that the bell curve of penis size of different races are different. Apparently, in US, White and Black guys say Asians have smaller penis (on average, to be scientifically exact, not a generalization for all case-by-case comparisons), do not seem to be racist comments ( or people will not bring it up). So if there are differences between races, in many different aspects, why it cannot be intelligence as well?

Of course, nobody wants to be called “Stupid”. However, differences in intelligence is not just about being smart or stupid. Human intelligence is a very complex thing, and cannot just be measured by SAT test scores and IQ. Intelligence applies to all skills, especially human skills such as reading, writing, social skills, artistic skills and many others. While tests may show certain race have a lower IQ on average, just like other aspects of what identifies a race, such as skin color, height, even penis size, it does not decide who is superior, and who is inferior. All races were well adapted to their own isolated environment. And now the world is a melting pot, so that by understanding the differences between races, it can be potentially very helpful.

I believe many people will still disagree. But one thing is interesting, in computer games, different races have different born abilities. Night elf have more spirit and agility and Tauren, which have more stamina and power. Perhaps, in order to be politically correct, we should not do science which could be taken advantage by racists, and games should create all races equal.

Talking about equal, equal does not need to be based on everyone is created identical. Some people are born to be artists, others engineers, other scientists.

The last thing is, scientifically, this “race and intelligence” hypothesis has not been proven wrong yet. So what if it is true? If you say it is false, I doubt any scientist can provide solid evidence either. If Africans are really genetically different, and the situation in Africa has its genetic basis, isn’t a good thing that now we know? So Africans can then improve themselves based on scientific facts. If scientists are not allowed to do this kind of research, we never know.

On the other hand, developed world do want Africa to be better right? Or are they afraid that Africa would find their way out?

Download the Watson Interview in PDF




新闻周刊Newsweek本周发表了”Troubled Waters”(问题水源)一文,首先就说中国。人口:十三亿;危机:污染。文章花了不少篇幅介绍世界各地水源的问题。

When you look more deeply into China’s water supply, however, you’ll see plenty to worry about. The government has long known what the Yangze is polluted….An April report by the World Wildlife Fund and two Chinese agencies found that damage to the river’s ecosystem is largely irreversible….











方舟子的新语丝最近发表了这篇文章,说的是英国的Operation Charm要打击中医药里面使用濒危动植物的做法。对于此事件,我想做以下评论。

首先表示对operation charm的支持。



Traditional Chinese Medicine

Operation Charm wants to stop the illegal trade in Traditional Chinese Medicines. This trade is rapidly expanding in many Western countries. Most of these medicines are made from herbs and other sustainable sources and are sold legally, but a minority are made from endangered species of animals and plants and the sale of these is illegal.

Traditional Chinese Medicine is part of an ancient culture, which is respected by Operation Charm, and we are working with the Chinese community and Chinese Medicine traders to stop the sale of endangered species products in London.

作者利用这个,下出一下结论: 引用:



请看这些 出国的中医生和中药商们为我们国家到底赢得了什么“荣誉”?


1) 方已经丧失基本的逻辑能力,因为此文档和此行动,不能作为证据表明中医没有赢得荣誉。此行动和文档,与中医是否有荣誉是完全没有任何关联的,不能互相证明。

2) 方没有丧失逻辑能力,而是精于辩论。之所以用这个来事件来打击中医和支持自己,是因为普通人不太能辨别此论据不能证明方的论点的事实。


!!!铁线虫 Gordian worms!!!


我仍然记得小时候,可能四五岁的时候,见到的铁线虫。这种可怕的虫子几乎给我的幼年制造了心灵创伤。Google Video里面有一个视频,说的是,据说铁线虫在蟋蟀体内成长成熟之后,就会向蟋蟀注射一种化合物,对蟋蟀进行“洗脑”。蟋蟀被洗脑后,跳入水中自杀,但是铁线虫却自由了,可以交配繁殖。



本来对中医是不提倡不反对。 但是这样的文章看多了,不免反感。 比如:


显然说明作者缺乏基本科学素养。按照这个逻辑,现代科学也不能说明“神创论 ”不科学,只能说明“神创论”是不同于现代科学的“科学”。类似还可以推倒到FLG之类。

又说,有人用MRI来研究针灸后脑图的变化,出了“专著”。 但是,专著是不需要peer review的。在一些好的期刊上发出来,都还有点说服力。


另外似乎是有效的。据说美国有兽医对狗进行针灸(狗的穴位是怎么定出来的??),有效果,止痛和治拉肚子之类的。虽然用针灸,但是很大程度上不是基于 传统中医吧?中医什么时候把动物的穴位和经络研究出来了?如果这个针灸不是对应穴位和经络也有效果,那么说明也许穴位和经络其实不存在?








  • 海胆(Sea Urchin)的基因组全序列被测出来了。海胆被认为是一个很好的模式生物,特别是在发育生物学方面。据说很多重要的研究也使用了海胆。但是遗憾的是以前似乎从来没有听说过海胆是这么重要呢?
  • Shigella降解细胞骨架,以便在细胞内活动。
  • 南部中国已经成为世界科学家心目中的流行病发源地?Science Podcast采访以为科学家,讨论可能的流感大流行,传播会非常快。这位科学家说,例如,流感可能会从South China开始,那是从以前的经验来看常见的发源地。一两天就可能传播到世界各地。但是从SARS,到禽流感,那一个不是和南部中国牵涉在一起的呢?比如广州,香港,福建。传说福建型禽流感变种目前到处都可以找到。而以前也见过一个科学家追溯SARS的传播,也是追踪到广东的某地。另外这个科学家也谈到,缺乏科学依据可以表明,洗手可以预防流感,虽然洗手是一件好事。
  • 国际质疑中国在禽流感方面的说法。前段时间已经在传言,中美科学家“吵架”。香港和美国科学家认为,目前在南部中国传播的禽流感已经发生变异。于是WTO要求中国提供样本,并贡献信息。中国科学家否认病毒发生变异。于是口水战开始。更有报道指出,虽然去年中国就承诺提供04到05年在中国传播的禽流感病毒的20个样本,但是样本仍旧还没有被邮寄到国际实验室。PNAS网上刊发的文章甚至带来新华网专题报道国务院新闻办的新闻发布会
  • 关于动物保护主义者和科学家受到的威胁的讨论继续
  • 图片

Most User Un-Friendly Phylogenetic Program Found!

And the winner is PAML(Phylogenetic Analysis by Maximum Likelihood) by Ziheng Yang!

I thought BioX is the best “bridge” between different programs because it supports so many different format. But PHYLIP and PAUP* format sequences generated by BioX are NOT readable by PAML’s yn00 program, although PAML claim to support PHYLIP and PAUP* nexus.

Well, maybe it is because me who hasn’t found a good way to do this. But you have to write control file for the program to run. And basically every sequence you are going to run, kind of need a different control file. And this is really unbelievable.

可以死而复生的细菌; E. coli超级计算机

Nature上报道了早已知道的Deinococcus radiodurans修复支离破碎的染色体机理的文章。这个极端细菌,即使染色体断裂为几百个片段,仍然可以从新修复,死而复生。它的这个能力已经被发现50多年,但是机理一直是一个谜。

Terra Soft据说要用Cell处理器构建超级计算机,这将是第一台使用Cell的超级计算机,名字叫做E. coli

Pretty interesting, huh.

Nobel Prize Winner 2006, Physiology/Medicine

Nobel Prize Winner



  • 可能通过体液,例如唾液传染的Prion可能被发现了。他们观察到鹿子之间有这种传播。
  • E. coli的”性与毒性”,进化的角度(Molecular Microbiology (2006) 60(5), 1136-1151)。文中作者再次质疑传统的Phylogenetic Approaches是否适用于E. coli。即使按照作者的看法,E.coli也并非重组得很频繁。如果这些方法,比如Maximum Likelihood之类,不适用于E.coli的话,那么这些方法可以说基本上不适用于至少一半的细菌?
  • Science上的这篇文章又谈到生命树。达尔文最先的草稿上画的“树”影响了一代又一代的科学家。尽管越来越多的人认为,或许Life of Tree根本就不存在也无法重构,或者如Nature上一篇文章假想的生命树并非树而是一个环,仍然有很多人继续为重构生命树努力。或许对于多细胞生物来说,生命树的构建要容易很多。或者如果你只打算把分辨率定为到Species的话,这个事情还是可以做一做的。
  • 寄生植物的嗅觉

Compile LDhat 0.2 on Intel Mac

LDhat is a package for recombination detection. It is written in C and no GUI is available.

The official website provide DOS executables, which I suppose they meant Windows command line executables. But they also provided source package with makefile. But if you make, it will fail. It will tell you it can’t find malloc.h. But after a little bit google, malloc.h turns out to be obsolete. and “including stdlib.h should take care of what malloc.h used to handle”. So you will need to comment out the include line in two files you will see when you make, by using “/*  */”. After that it would compile just fine.

Enjoy life without Windows again.

UPDATE: The LDhat I compiled did not function properly. Even if I have malloc.h linked to /usr/include, convert will quit because of segment fault while reading sequences. This is not because of the sequence file because it quit reading sample data included with the package.

UPDATE2: LDhat compiled for Intel Mac this way seems working, except  it seems sometimes it could not load all the sequence and segment fault. It seems this happens when there are 8 sequence types/sequences. Other than that, it is working for me.

Compile SITES for your Intel Mac

SITES is a software by Hey’s lab at Rutgers University. Like some other softwares, you have to compile it yourself for it to be able to run on Intel Macs.

Instruction(First one is easiest, but might not produce a working binary. Later one require you to download the makefile I wrote, but it definitely works, because I tested it.):

Download the source from SITES official website. Extract the archive. From terminal, change directory to where these .c and .h files are.

use command

gcc -O2 *.c

And you will get a a.out file. Change the name of a.out to SITES or other name you want it. Chmod 755 to make it executable. Now you can run it from command line. Mac OS X is a better environment for command line programs. So even we could run Windows on Intel Mac with Boot Camp or Parallels, I would prefer to use our very best native UNIX environment on Mac OS X.

If it doesn’t work properly, then try download the attached Makefile. Put this file in the same directory as source code, and in terminal, type “make”, then you will get the SITES executable!



当然我这个网站的统计功能还是比较不错的,至少可以看到别人如果是通过搜索引擎是怎么来到我这个网站的。最近用A9比较多,因为一来可以获得Amazon.com的折扣,二来最近不少经验表明Windows Live的搜索结果比Google准确一些。

最近有好几个访问者是通过搜索关键词”mrbayes”, “mrbayes intel mac”等类似关键词过来的。于是我就搜索后者看看我的记录是不是比较靠前。果然在A9上就排在第一位。不过Google上则是第三页还是四页上去了。由于MrBayes的官方网站至今没有Intel的版本编译放出,所以我也揣测有不少人可能会希望在Intel Mac上用原生的执行程序吧。所以这一次A9/Windows Live的搜索结果又一次战胜了Google,因为我的Blog里面就是专门说怎么在Intel Mac下面编译MrBayes的。








阅读学习Fundamentals of Molecula Eolution(Graur and Li)中,有些关于积累的微弱优势如何在群体中积累、扩大频率的疑问得到一些解答。好书。

Say NO to Green Peace International

In my memories, Green Peace International is a organization that cares our planet, fight against pollution and all kinds of things that endanger our environment. A recent read about their opinion on genetic engineering (GE) and genetic modified (GM) organisms changed my mind.

Green Peace International (GPI) is opposed of GE. They published articles on the web, write “paper” saying that GE is outdated and failed and should not be used; genetic modified (GM) organisms should not be released into the environment.

In this paper, “50 years since the double helix: Genetic Engineering is crude and old-fashioned”, GPI basically stated that 1) the basic theory “Central Dogma” that GE is based on has undergone so many changes so that it is not a good foundation for GE any more; 2) gene expression is far more complicated that people thought, and GE simply randomly insert a single foreign gene into the organism and it is not acceptable; 3) GM food have not been fully tested and their impact on human and environment is unpredictable.

While they might have made some strong arguments, they fail to see that GE has also been changing while discoveries being made. It is not only industry is doing GE and GM food, scientists in universities and institutes are doing it too. Who modified central dogma? Scientists in universities. And these scientists are also changing the way of doing GE. So GE is NOT old-fashioned and it is GPI and other people who blindly fight against GE are old-fashioned: in their mind, GE is the same as 50 years ago.

Introduced genes into GM organisms are also not exactly “pollution”. Maybe bacterial genes such as Bt can be considered, to some extent, “pollution”, but there are many other cases in which people introduce one gene from one species of plant to another species of plant. Also, these genes are ALL naturally exisiting in nature, none of them are artificially made (we don’t have that technology yet either). Even we don’t insert foreign genes into crops, there are many plant pathogenic bacteria and viruses who have the ability to insert their own genome components into plants and it is HAPPENING. So the “pollution” GPI defined, is even occuring in nature, and I cannot imagine they could start a campaign to stop that.

So, GE is not something completely artificial. Many techniques scientist utilize to deliver foreign genes are using natural organisms, for instance plant pathogenic bacteria and viruses because they have the ability and they have been delivering genes into plants’ genomes (for millions of years). And genes that are delivered are basically naturally exisiting genes. GE is elvoving together with other molecular biology discoveries and scientists are trying to make it safer and more efficient.

I have to say GPI is a great disappointment. I knew them since childhood, and I believe they have done a lot of good things. But any organization that goes extreme is a hazard to our world. I have mention that in the paper I just mentioned, their references are quite funny. They did cite many important papers, and many published in Science and Nature. But they also cited quite a large number of articles from New Scientist. New Scientist is NOT a scientific journal. According to Wikipedia:

New Scientist is a weekly international science magazine covering recent developments in science and technology for a general English-speaking audience. As well as covering current events and news from the scientific community, the magazine often features speculative articles, ranging from the philosophical to the technical.

It is not a peer-reviewed scientific journal, but it is widely read by both nonscientists and scientists as a way of keeping track of developments outside their own fields of study or areas of interest.

Please pay attention to the bold words in the citation above. Not only does New Scientist is not scientific journal, it is not neutral either. Their editors’ point of view decide how they are going to influence the public (without responsibility). A little google will tell you that New Scientist has already chosen their position to be NO to the GE. And you are not expected to see a REAL neutral article analysing the GE issue on such a magazine. GPI’s citing this magazine only makes their “paper” making no sense.

General public, of course, do not know much about molecular biology and what scientists are doing. And their opinions are just very easily manipulated by organization and magazine like GPI and New Scientist. While it is true that GE has potential environmental and health issues, and GE needs to be improved along the way, and also GE might not be ready for large scale commercial production, I am extremely disappointed to see organization like GPI to treat GE as it is a nuke, or a terrorist.

I will not donate money to GPI because I am not one of them.